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Chen H, Li N, Cai Y, Ma C, Ye Y, Shi X, Guo J, Han Z, Liu Y, Wei X. Exosomes in neurodegenerative diseases: Therapeutic potential and modification methods. Neural Regen Res 2026; 21:478-490. [PMID: 40326981 DOI: 10.4103/nrr.nrr-d-24-00720] [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: 08/06/2024] [Accepted: 10/14/2024] [Indexed: 05/07/2025] Open
Abstract
In recent years, exosomes have garnered extensive attention as therapeutic agents and early diagnostic markers in neurodegenerative disease research. Exosomes are small and can effectively cross the blood-brain barrier, allowing them to target deep brain lesions. Recent studies have demonstrated that exosomes derived from different cell types may exert therapeutic effects by regulating the expression of various inflammatory cytokines, mRNAs, and disease-related proteins, thereby halting the progression of neurodegenerative diseases and exhibiting beneficial effects. However, exosomes are composed of lipid bilayer membranes and lack the ability to recognize specific target cells. This limitation can lead to side effects and toxicity when they interact with non-specific cells. Growing evidence suggests that surface-modified exosomes have enhanced targeting capabilities and can be used as targeted drug-delivery vehicles that show promising results in the treatment of neurodegenerative diseases. In this review, we provide an up-to-date overview of existing research aimed at devising approaches to modify exosomes and elucidating their therapeutic potential in neurodegenerative diseases. Our findings indicate that exosomes can efficiently cross the blood-brain barrier to facilitate drug delivery and can also serve as early diagnostic markers for neurodegenerative diseases. We introduce the strategies being used to enhance exosome targeting, including genetic engineering, chemical modifications (both covalent, such as click chemistry and metabolic engineering, and non-covalent, such as polyvalent electrostatic and hydrophobic interactions, ligand-receptor binding, aptamer-based modifications, and the incorporation of CP05-anchored peptides), and nanomaterial modifications. Research into these strategies has confirmed that exosomes have significant therapeutic potential for neurodegenerative diseases. However, several challenges remain in the clinical application of exosomes. Improvements are needed in preparation, characterization, and optimization methods, as well as in reducing the adverse reactions associated with their use. Additionally, the range of applications and the safety of exosomes require further research and evaluation.
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Affiliation(s)
- Hongli Chen
- Institute of Biomedical Engineering, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- State Key Laboratory of Separation Membrane and Membrane Process & Tianjin Key Laboratory of Optoelectronic Detection Technology and Systems, School of Life Sciences, Tiangong University, Tianjin, China
| | - Na Li
- State Key Laboratory of Separation Membrane and Membrane Process & Tianjin Key Laboratory of Optoelectronic Detection Technology and Systems, School of Life Sciences, Tiangong University, Tianjin, China
| | - Yuanhao Cai
- State Key Laboratory of Separation Membrane and Membrane Process & Tianjin Key Laboratory of Optoelectronic Detection Technology and Systems, School of Life Sciences, Tiangong University, Tianjin, China
- School of Intelligent Information Engineering, Medicine & Technology College of Zunyi Medical University, Zunyi, Guizhou Province, China
| | - Chunyan Ma
- State Key Laboratory of Separation Membrane and Membrane Process & Tianjin Key Laboratory of Optoelectronic Detection Technology and Systems, School of Life Sciences, Tiangong University, Tianjin, China
| | - Yutong Ye
- State Key Laboratory of Separation Membrane and Membrane Process & Tianjin Key Laboratory of Optoelectronic Detection Technology and Systems, School of Life Sciences, Tiangong University, Tianjin, China
| | - Xinyu Shi
- State Key Laboratory of Separation Membrane and Membrane Process & Tianjin Key Laboratory of Optoelectronic Detection Technology and Systems, School of Life Sciences, Tiangong University, Tianjin, China
| | - Jun Guo
- State Key Laboratory of Separation Membrane and Membrane Process & Tianjin Key Laboratory of Optoelectronic Detection Technology and Systems, School of Life Sciences, Tiangong University, Tianjin, China
| | - Zhibo Han
- Tianjin Key Laboratory of Engineering Technologies for Cell Pharmaceuticals, National Engineering Research Center of Cell Products, AmCellGene Co., Ltd., Tianjin, China
| | - Yi Liu
- State Key Laboratory of Separation Membrane and Membrane Process & Tianjin Key Laboratory of Optoelectronic Detection Technology and Systems, School of Life Sciences, Tiangong University, Tianjin, China
| | - Xunbin Wei
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Cancer Hospital & Institute, International Cancer Institute, Institute of Medical Technology, Peking University Health Science Center, Department of Biomedical Engineering, Peking University, Beijing, China
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2
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Münz C, Campbell GR, Esclatine A, Faure M, Labonte P, Lussignol M, Orvedahl A, Altan-Bonnet N, Bartenschlager R, Beale R, Cirone M, Espert L, Jung J, Leib D, Reggiori F, Sanyal S, Spector SA, Thiel V, Viret C, Wei Y, Wileman T, Wodrich H. Autophagy machinery as exploited by viruses. AUTOPHAGY REPORTS 2025; 4:27694127.2025.2464986. [PMID: 40201908 PMCID: PMC11921968 DOI: 10.1080/27694127.2025.2464986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2024] [Revised: 01/17/2025] [Accepted: 01/27/2025] [Indexed: 04/10/2025]
Abstract
Viruses adapt and modulate cellular pathways to allow their replication in host cells. The catabolic pathway of macroautophagy, for simplicity referred to as autophagy, is no exception. In this review, we discuss anti-viral functions of both autophagy and select components of the autophagy machinery, and how viruses have evaded them. Some viruses use the membrane remodeling ability of the autophagy machinery to build their replication compartments in the cytosol or efficiently egress from cells in a non-lytic fashion. Some of the autophagy machinery components and their remodeled membranes can even be found in viral particles as envelopes or single membranes around virus packages that protect them during spreading and transmission. Therefore, studies on autophagy regulation by viral infections can reveal functions of the autophagy machinery beyond lysosomal degradation of cytosolic constituents. Furthermore, they can also pinpoint molecular interactions with which the autophagy machinery can most efficiently be manipulated, and this may be relevant to develop effective disease treatments based on autophagy modulation.
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Affiliation(s)
- Christian Münz
- Viral Immunobiology, Institute of Experimental Immunology, University of Zürich, ZürichSwitzerland
| | - Grant R Campbell
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of SD, Vermillion, SD, USA
| | - Audrey Esclatine
- Université Paris-Saclay, CEA, CNRS, 10 Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Mathias Faure
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Universite Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007Lyon, France
| | - Patrick Labonte
- eINRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Canada
| | - Marion Lussignol
- Université Paris-Saclay, CEA, CNRS, 10 Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Anthony Orvedahl
- Department of Pediatrics, Washington University in St. Louis, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Nihal Altan-Bonnet
- Laboratory of Host-Pathogen Dynamics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ralf Bartenschlager
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Division Virus-Associated Carcinogenesis, Heidelberg, Germany
- German Centre for Infection Research, Heidelberg partner site, Heidelberg, Germany
| | - Rupert Beale
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London, UK
- Division of Medicine, University College London, London, UK
| | - Mara Cirone
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Lucile Espert
- University of Montpellier, Montpellier, France
- CNRS, Institut de Recherche enInfectiologie deMontpellier (IRIM), Montpellier, France
| | - Jae Jung
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - David Leib
- Guarini School of Graduate and Advanced Studies at Dartmouth, Hanover, NH, USA
| | - Fulvio Reggiori
- Department of Biomedicine, Aarhus University, Ole Worms Allé 4, Aarhus C, Denmark
| | - Sumana Sanyal
- Sir William Dunn School of Pathology, South Parks Road, University of Oxford, Oxford, UK
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Stephen A. Spector
- Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Rady Children’s Hospital, San Diego, CA, USA
| | - Volker Thiel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland; Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Christophe Viret
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Universite Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007Lyon, France
| | - Yu Wei
- Institut Pasteur-Theravectys Joint Laboratory, Department of Virology, Institut Pasteur, Université Paris Cité, Paris, France
| | - Thomas Wileman
- Norwich Medical School, University of East Anglia
- Quadram Institute Bioscience, Norwich Research Park, Norfolk, UK
| | - Harald Wodrich
- Laboratoire de Microbiologie Fondamentale et Pathogénicité, MFP CNRS UMR, Université de Bordeaux, Bordeaux, France
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Choi JC. Perinuclear organelle trauma at the nexus of cardiomyopathy pathogenesis arising from loss of function LMNA mutation. Nucleus 2025; 16:2449500. [PMID: 39789731 PMCID: PMC11730615 DOI: 10.1080/19491034.2024.2449500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2024] [Revised: 12/22/2024] [Accepted: 12/30/2024] [Indexed: 01/12/2025] Open
Abstract
Over the past 25 years, nuclear envelope (NE) perturbations have been reported in various experimental models with mutations in the LMNA gene. Although the hypothesis that NE perturbations from LMNA mutations are a fundamental feature of striated muscle damage has garnered wide acceptance, the molecular sequalae provoked by the NE damage and how they underlie disease pathogenesis such as cardiomyopathy (LMNA cardiomyopathy) remain poorly understood. We recently shed light on one such consequence, by employing a cardiomyocyte-specific Lmna deletion in vivo in the adult heart. We observed extensive NE perturbations prior to cardiac function deterioration with collateral damage in the perinuclear space. The Golgi is particularly affected, leading to cytoprotective stress responses that are likely disrupted by the progressive deterioration of the Golgi itself. In this review, we discuss the etiology of LMNA cardiomyopathy with perinuclear 'organelle trauma' as the nexus between NE damage and disease pathogenesis.
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Affiliation(s)
- Jason C. Choi
- Center for Translational Medicine, Department of Medicine, Thomas Jefferson University, Philadelphia, PA, USA
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Shahin R, Jaafreh S, Azzam Y. Tracking protein kinase targeting advances: integrating QSAR into machine learning for kinase-targeted drug discovery. Future Sci OA 2025; 11:2483631. [PMID: 40181786 PMCID: PMC11980485 DOI: 10.1080/20565623.2025.2483631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 03/06/2025] [Indexed: 04/05/2025] Open
Abstract
Protein kinases are vital drug targets, yet designing selective inhibitors is challenging, compounded by resistance and kinome complexity. This review explores Quantitative Structure-Activity Relationship (QSAR) modeling for kinase drug discovery, focusing on integrating traditional QSAR with machine learning (ML)-CNNs, RNNs-and structural data. Methods include structural databases, docking, and deep learning QSAR. Key findings show ML-integrated QSAR significantly improves selective inhibitor design for CDKs, JAKs, PIM kinases. The IDG-DREAM challenge exemplifies ML's potential for accurate kinase-inhibitor interaction prediction, outperforming traditional methods and enabling inhibitors with enhanced selectivity, efficacy, and resistance mitigation. QSAR combined with advanced computation and experimental data accelerates kinase drug discovery, offering transformative precision medicine potential. This review highlights deep learning-enhanced QSAR's novelty in automating feature extraction and capturing complex relationships, surpassing traditional QSAR, while emphasizing interpretability and experimental validation for clinical translation.
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Affiliation(s)
- Rand Shahin
- Drug Design Unit, Department of Pharmaceutical Chemistry, Hashemite University, Zarqa, Jordan
| | - Sawsan Jaafreh
- Department of Chemistry, The Hashemite University, Zarqa, Jordan
| | - Yusra Azzam
- Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
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5
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Hiruthyaswamy SP, Bose A, Upadhyay A, Raha T, Bhattacharjee S, Singha I, Ray S, Nicky Macarius NM, Viswanathan P, Deepankumar K. Molecular signaling pathways in osteoarthritis and biomaterials for cartilage regeneration: a review. Bioengineered 2025; 16:2501880. [PMID: 40336219 PMCID: PMC12064066 DOI: 10.1080/21655979.2025.2501880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Revised: 03/07/2025] [Accepted: 04/04/2025] [Indexed: 05/09/2025] Open
Abstract
Osteoarthritis is a prevalent degenerative joint disease characterized by cartilage degradation, synovial inflammation, and subchondral bone alterations, leading to chronic pain and joint dysfunction. Conventional treatments provide symptomatic relief but fail to halt disease progression. Recent advancements in biomaterials, molecular signaling modulation, and gene-editing technologies offer promising therapeutic strategies. This review explores key molecular pathways implicated in osteoarthritis, including fibroblast growth factor, phosphoinositide 3-kinase/Akt, and bone morphogenetic protein signaling, highlighting their roles in chondrocyte survival, extracellular matrix remodeling, and inflammation. Biomaterial-based interventions such as hydrogels, nanoparticles, and chitosan-based scaffolds have demonstrated potential in enhancing cartilage regeneration and targeted drug delivery. Furthermore, CRISPR/Cas9 gene editing holds promise in modifying osteoarthritis-related genes to restore cartilage integrity. The integration of regenerative biomaterials with precision medicine and molecular therapies represents a novel approach for mitigating osteoarthritis progression. Future research should focus on optimizing biomaterial properties, refining gene-editing efficiency, and developing personalized therapeutic strategies. The convergence of bioengineering and molecular science offers new hope for improving joint function and patient quality of life in osteoarthritis management.
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Affiliation(s)
- Samson Prince Hiruthyaswamy
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Arohi Bose
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Ayushi Upadhyay
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Tiasa Raha
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Shangomitra Bhattacharjee
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Isheeta Singha
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Swati Ray
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | | | - Pragasam Viswanathan
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Kanagavel Deepankumar
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
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6
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Nair A, Khanna J, Kler J, Ragesh R, Sengupta K. Nuclear envelope and chromatin choreography direct cellular differentiation. Nucleus 2025; 16:2449520. [PMID: 39943681 PMCID: PMC11834525 DOI: 10.1080/19491034.2024.2449520] [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: 10/01/2024] [Revised: 12/28/2024] [Accepted: 12/30/2024] [Indexed: 02/20/2025] Open
Abstract
The nuclear envelope plays an indispensable role in the spatiotemporal organization of chromatin and transcriptional regulation during the intricate process of cell differentiation. This review outlines the distinct regulatory networks between nuclear envelope proteins, transcription factors and epigenetic modifications in controlling the expression of cell lineage-specific genes during differentiation. Nuclear lamina with its associated nuclear envelope proteins organize heterochromatin via Lamina-Associated Domains (LADs), proximal to the nuclear periphery. Since nuclear lamina is mechanosensitive, we critically examine the impact of extracellular forces on differentiation outcomes. The nuclear envelope is spanned by nuclear pore complexes which, in addition to their central role in transport, are associated with chromatin organization. Furthermore, mutations in the nuclear envelope proteins disrupt differentiation, resulting in developmental disorders. Investigating the underlying nuclear envelope controlled regulatory mechanisms of chromatin remodelling during lineage commitment will accelerate our fundamental understanding of developmental biology and regenerative medicine.
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Affiliation(s)
- Anjitha Nair
- Chromosome Biology Lab (CBL), Indian Institute of Science Education and Research (IISER) Pune, Maharashtra, India
| | - Jayati Khanna
- Chromosome Biology Lab (CBL), Indian Institute of Science Education and Research (IISER) Pune, Maharashtra, India
| | - Jashan Kler
- Chromosome Biology Lab (CBL), Indian Institute of Science Education and Research (IISER) Pune, Maharashtra, India
| | - Rohith Ragesh
- Chromosome Biology Lab (CBL), Indian Institute of Science Education and Research (IISER) Pune, Maharashtra, India
| | - Kundan Sengupta
- Chromosome Biology Lab (CBL), Indian Institute of Science Education and Research (IISER) Pune, Maharashtra, India
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Ji J, Gong C, Lu G, Zhang J, Liu B, Liu X, Lin J, Wang P, Thomas BB, Humayun MS, Zhou Q. Potential of ultrasound stimulation and sonogenetics in vision restoration: a narrative review. Neural Regen Res 2025; 20:3501-3516. [PMID: 39688549 PMCID: PMC11974640 DOI: 10.4103/nrr.nrr-d-24-00841] [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: 07/27/2024] [Revised: 11/04/2024] [Accepted: 11/21/2024] [Indexed: 12/18/2024] Open
Abstract
Vision restoration presents a considerable challenge in the realm of regenerative medicine, while recent progress in ultrasound stimulation has displayed potential as a non-invasive therapeutic approach. This narrative review offers a comprehensive overview of current research on ultrasound-stimulated neuromodulation, emphasizing its potential as a treatment modality for various nerve injuries. By examining of the efficacy of different types of ultrasound stimulation in modulating peripheral and optic nerves, we can delve into their underlying molecular mechanisms. Furthermore, the review underscores the potential of sonogenetics in vision restoration, which involves leveraging pharmacological and genetic manipulations to inhibit or enhance the expression of related mechanosensitive channels, thereby modulating the strength of the ultrasound response. We also address how methods such as viral transcription can be utilized to render specific neurons or organs highly responsive to ultrasound, leading to significantly improved therapeutic outcomes.
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Affiliation(s)
- Jie Ji
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Chen Gong
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
- USC Roski Eye Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Gengxi Lu
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
- USC Roski Eye Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Junhang Zhang
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
- USC Roski Eye Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Baoqiang Liu
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Xunan Liu
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Junhao Lin
- Thomas Lord Department of Computer Science, University of Southern California, Los Angeles, CA, USA
| | | | - Biju B. Thomas
- USC Roski Eye Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Mark S. Humayun
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
- USC Roski Eye Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Qifa Zhou
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
- USC Roski Eye Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
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Yao H, Wu R, Du D, Ai F, Yang F, Li Y, Qi S. Flavonoids from Polypodium hastatum as neuroprotective agents attenuate cerebral ischemia/reperfusion injury in vitro and in vivo via activating Nrf2. Redox Rep 2025; 30:2440204. [PMID: 39702961 DOI: 10.1080/13510002.2024.2440204] [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] [Indexed: 12/21/2024] Open
Abstract
OBJECTIVES Cerebral ischemic stroke is a leading cause of death worldwide. Though timely reperfusion reduces the infarction size, it exacerbates neuronal apoptosis due to oxidative stress. Nuclear factor erythroid 2-related factor 2 (Nrf2) is a transcription factor regulating the expression of antioxidant enzymes. Activating Nrf2 gives a therapeutic approach to ischemic stroke. METHODS Herein we explored flavonoids identified from Polypodium hastatum as Nrf2 activators and their protective effects on PC12 cells injured by oxygen and glucose deprivation/restoration (OGD/R) as well as middle cerebral artery occlusion (MCAO) mice. RESULTS The results showed among these flavonoids, AAKR significantly improved the survival of PC12 cells induced by OGD/R and activated Nrf2 in a Keap1-dependent manner. Further investigations have disclosed AAKR attenuated oxidative stress, mitochondrial dysfunction and following apoptosis resulting from OGD/R. Meanwhile, activation of Nrf2 by AAKR was involved in the protective effects. Finally, it was found that AAKR could protect MCAO mice brains against ischemia/reperfusion injury via activating Nrf2. DISCUSSION This investigation could provide lead compounds for the discovery of novel Nrf2 activators targeting ischemia/reperfusion injury.
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Affiliation(s)
- Huankai Yao
- Department of Microbial and Biochemical Pharmacy, School of Pharmacy & Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, People's Republic of China
| | - Ruiqing Wu
- Department of Microbial and Biochemical Pharmacy, School of Pharmacy & Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, People's Republic of China
| | - Dan Du
- Department of Microbial and Biochemical Pharmacy, School of Pharmacy & Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, People's Republic of China
| | - Fengwei Ai
- Department of Microbial and Biochemical Pharmacy, School of Pharmacy & Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, People's Republic of China
| | - Feng Yang
- School of Stomatology, Xuzhou Medical University, Xuzhou, People's Republic of China
| | - Yan Li
- Department of Microbial and Biochemical Pharmacy, School of Pharmacy & Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, People's Republic of China
| | - Suhua Qi
- School of Medical Technology & Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, People's Republic of China
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Ramon A, Ni M, Predeina O, Gaffey R, Kunz P, Onuoha S, Sormanni P. Prediction of protein biophysical traits from limited data: a case study on nanobody thermostability through NanoMelt. MAbs 2025; 17:2442750. [PMID: 39772905 PMCID: PMC11730357 DOI: 10.1080/19420862.2024.2442750] [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: 10/04/2024] [Revised: 12/10/2024] [Accepted: 12/11/2024] [Indexed: 01/11/2025] Open
Abstract
In-silico prediction of protein biophysical traits is often hindered by the limited availability of experimental data and their heterogeneity. Training on limited data can lead to overfitting and poor generalizability to sequences distant from those in the training set. Additionally, inadequate use of scarce and disparate data can introduce biases during evaluation, leading to unreliable model performances being reported. Here, we present a comprehensive study exploring various approaches for protein fitness prediction from limited data, leveraging pre-trained embeddings, repeated stratified nested cross-validation, and ensemble learning to ensure an unbiased assessment of the performances. We applied our framework to introduce NanoMelt, a predictor of nanobody thermostability trained with a dataset of 640 measurements of apparent melting temperature, obtained by integrating data from the literature with 129 new measurements from this study. We find that an ensemble model stacking multiple regression using diverse sequence embeddings achieves state-of-the-art accuracy in predicting nanobody thermostability. We further demonstrate NanoMelt's potential to streamline nanobody development by guiding the selection of highly stable nanobodies. We make the curated dataset of nanobody thermostability freely available and NanoMelt accessible as a downloadable software and webserver.
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Affiliation(s)
- Aubin Ramon
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Mingyang Ni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Olga Predeina
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Rebecca Gaffey
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Patrick Kunz
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
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Xu Z, Asakawa S. Release and degradation of dissolved environmental RNAs from zebrafish cells. RNA Biol 2025; 22:1-12. [PMID: 40167163 PMCID: PMC12026185 DOI: 10.1080/15476286.2025.2486281] [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: 12/28/2024] [Revised: 02/27/2025] [Accepted: 03/21/2025] [Indexed: 04/02/2025] Open
Abstract
The sources and degradation profiles of dissolved environmental RNAs from fish in water remain unknown. In this study, laboratory experiments and mathematical modelling were conducted to investigate the permeability of RNA extracted from zebrafish cells through filters, the release of dissolved environmental RNAs from live and dying zebrafish cells, and the degradation of RNA extracted from zebrafish cells in a non-sterile aqueous environment. This research aimed to provide biological and ecological insights into fish RNAs dissolved in water. The results showed that most of the RNA extracted from zebrafish cells was detected in the filtrates after passage through 0.45 µm filters. Over the course of the 6-day experiment, dynamic levels of the RNAs in the liquid environment containing live or dying zebrafish cells were determined. The release and degradation rates of dissolved environmental RNA from zebrafish cells were calculated using mathematical modelling. RNA extracted from zebrafish cells degraded in non-sterile water in the tubes, and after 2 months, more than 15% of the RNAs in the water remained detectable. The half-life of the RNA in the tubes was approximately 20 ~ 43 days. The modelling results suggest that the levels of the dissolved environmental fish RNAs in natural waters or aquariums could be so low that it would be difficult to detect them using current techniques. The results obtained in this study will help develop new methods for measuring the dynamics of dissolved environmental fish RNAs in water and determining their significance.
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Affiliation(s)
- Zhongneng Xu
- Department of Ecology, Jinan University, Guangzhou, China
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, Japan
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11
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Yang J, Qureshi M, Kolli R, Peacock TP, Sadeyen JR, Carter T, Richardson S, Daines R, Barclay WS, Brown IH, Iqbal M. The haemagglutinin gene of bovine-origin H5N1 influenza viruses currently retains receptor-binding and pH-fusion characteristics of avian host phenotype. Emerg Microbes Infect 2025; 14:2451052. [PMID: 39803980 PMCID: PMC11776067 DOI: 10.1080/22221751.2025.2451052] [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: 09/27/2024] [Revised: 01/01/2025] [Accepted: 01/05/2025] [Indexed: 01/29/2025]
Abstract
Clade 2.3.4.4b H5N1 high pathogenicity avian influenza virus (HPAIV) has caused a panzootic affecting all continents except Australia, expanding its host range to several mammalian species. In March 2024, H5N1 HPAIV was first detected in dairy cattle and goats in the United States. Over 891 dairy farms across 16 states have tested positive until 25 December 2024, with zoonotic infections reported among dairy workers. This raises concerns about the virus undergoing evolutionary changes in cattle that could enhance its zoonotic potential. The Influenza glycoprotein haemagglutinin (HA) facilitates entry into host cells through receptor binding and pH-induced fusion with cellular membranes. Adaptive changes in HA modulate virus-host cell interactions. This study compared the HA genes of cattle and goat H5N1 viruses with the dominant avian-origin clade 2.3.4.4b H5N1 in the United Kingdom, focusing on receptor binding, pH fusion, and thermostability. All the tested H5N1 viruses showed binding exclusively to avian-like receptors, with a pH fusion of 5.9, outside the pH range associated with efficient human airborne transmissibility (pH 5.0-5.5). We further investigated the impact of emerging HA substitutions seen in the ongoing cattle outbreaks, but saw little phenotypic difference, with continued exclusive binding to avian-like receptor analogues and pHs of fusion above 5.8. This suggests that the HA genes from the cattle and goat outbreaks do not pose an enhanced threat compared to circulating avian viruses. However, given the rapid evolution of H5 viruses, continuous monitoring and updated risk assessments remain essential to understanding virus zoonotic and pandemic risks.
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Affiliation(s)
| | | | | | - Thomas P. Peacock
- The Pirbright Institute, Pirbright, UK
- Department of Infectious Disease, Imperial College London, London, UK
| | | | | | | | | | - Wendy S. Barclay
- Department of Infectious Disease, Imperial College London, London, UK
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12
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Valle J. Biofilm-associated proteins: from the gut biofilms to neurodegeneration. Gut Microbes 2025; 17:2461721. [PMID: 39898557 PMCID: PMC11792866 DOI: 10.1080/19490976.2025.2461721] [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] [Received: 10/25/2024] [Revised: 12/07/2024] [Accepted: 01/28/2025] [Indexed: 02/04/2025] Open
Abstract
Human microbiota form a biofilm with substantial consequences for health and disease. Numerous studies have indicated that microbial communities produce functional amyloids as part of their biofilm extracellular scaffolds. The overlooked interplay between bacterial amyloids and the host may have detrimental consequences for the host, including neurodegeneration. This work gives an overview of the biofilm-associated amyloids expressed by the gut microbiota and their potential role in neurodegeneration. It discusses the biofilm-associated proteins (BAPs) of the gut microbiota, maps the amyloidogenic domains of these proteins, and analyzes the presence of bap genes within accessory genomes linked with transposable elements. Furthermore, the evidence supporting the existence of amyloids in the gut are presented. Finally, it explores the potential interactions between BAPs and α-synuclein, extending the literature on amyloid cross-kingdom interactions. Based on these findings, this study propose that BAP amyloids act as transmissible catalysts, facilitating the misfolding, accumulation, and spread of α-synuclein aggregates. This review contributes to the understanding of complex interactions among the microbiota, transmissible elements, and host, which is crucial for developing novel therapeutic approaches to combat microbiota-related diseases and improve overall health outcomes.
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Affiliation(s)
- Jaione Valle
- Microbial Biotechnology Department, Instituto de Agrobiotecnología, CSIC-Gobierno de Navarra, Mutilva, Navarra, Spain
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13
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Lee H, Park H, Kwak K, Lee CE, Yun J, Lee D, Lee JH, Lee SH, Kang LW. Structural comparison of substrate-binding pockets of serine β-lactamases in classes A, C, and D. J Enzyme Inhib Med Chem 2025; 40:2435365. [PMID: 39714271 DOI: 10.1080/14756366.2024.2435365] [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: 07/10/2024] [Revised: 10/08/2024] [Accepted: 11/22/2024] [Indexed: 12/24/2024] Open
Abstract
β-lactams have been the most successful antibiotics, but the rise of multi-drug resistant (MDR) bacteria threatens their effectiveness. Serine β-lactamases (SBLs), among the most common causes of resistance, are classified as A, C, and D, with numerous variants complicating structural and substrate spectrum comparisons. This study compares representative SBLs of these classes, focusing on the substrate-binding pocket (SBP). SBP is kidney bean-shaped on the indented surface, formed mainly by loops L1, L2, and L3, and an additional loop Lc in class C. β-lactams bind in a conserved orientation, with the β-lactam ring towards L2 and additional rings towards the space between L1 and L3. Structural comparison shows each class has distinct SBP structures, but subclasses share a conserved scaffold. The SBP structure, accommodating complimentary β-lactams, determines the substrate spectrum of SBLs. The systematic comparison of SBLs, including structural compatibility between β-lactams and SBPs, will help understand their substrate spectrum.
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Affiliation(s)
- Hyeonmin Lee
- Department of Biological Sciences, Konkuk University, Seoul, Republic of Korea
| | - Hyunjae Park
- Department of Biological Sciences, Konkuk University, Seoul, Republic of Korea
| | - Kiwoong Kwak
- Department of Biological Sciences, Konkuk University, Seoul, Republic of Korea
| | - Chae-Eun Lee
- Department of Biological Sciences, Konkuk University, Seoul, Republic of Korea
| | - Jiwon Yun
- Department of Biological Sciences, Konkuk University, Seoul, Republic of Korea
| | - Donghyun Lee
- Department of Biological Sciences, Konkuk University, Seoul, Republic of Korea
| | - Jung Hun Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Lin-Woo Kang
- Department of Biological Sciences, Konkuk University, Seoul, Republic of Korea
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14
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Negi MS, Krishnan VP, Saraf N, Vijayraghavan U. Prp16 enables efficient splicing of introns with diverse exonic consensus elements in the short-intron rich Cryptococcus neoformans transcriptome. RNA Biol 2025; 22:1-14. [PMID: 40065603 PMCID: PMC11913375 DOI: 10.1080/15476286.2025.2477844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/24/2025] [Accepted: 03/04/2025] [Indexed: 03/14/2025] Open
Abstract
DEAH box splicing helicase Prp16 in budding yeast governs spliceosomal remodelling from the branching conformation (C complex) to the exon ligation conformation (C* complex). In this study, we examined the genome-wide functions of Prp16 in the short intron-rich genome of the basidiomycete yeast Cryptococcus neoformans. The presence of multiple introns per transcript with intronic features that are more similar to those of higher eukaryotes makes it a promising model for studying spliceosomal splicing. Using a promoter-shutdown conditional Prp16 knockdown strain, we uncovered genome-wide but substrate-specific roles in C. neoformans splicing. The splicing functions of Prp16 are dependent on helicase motifs I and II, which are conserved motifs for helicase activity. A small subset of introns spliced independent of Prp16 activity was investigated to discover that exonic sequences at the 5' splice site (5'SS) and 3' splice site (3'SS) with stronger affinity for U5 loop 1 are a common feature in these introns. Furthermore, short (60-100nts) and ultrashort introns (<60nts) prevalent in the C. neoformans transcriptome were more sensitive to Prp16 knockdown than longer introns, indicating that Prp16 is required for the efficient splicing of short and ultrashort introns. We propose that stronger U5 snRNA-pre-mRNA interactions enable efficient transition of the spliceosome from the first to the second catalytic confirmation in Prp16 knockdown, particularly for short introns and introns with suboptimal features. This study provides insights into fine-tuning spliceosomal helicase function with variations in cis-element features.
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Affiliation(s)
- Manendra Singh Negi
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Vishnu Priya Krishnan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Niharika Saraf
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Usha Vijayraghavan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
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15
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Rodrigues CS, Gaifem J, Pereira MS, Alves MF, Silva M, Padrão N, Cavadas B, Moreira-Barbosa C, Alves I, Marcos-Pinto R, Torres J, Lavelle A, Colombel JF, Sokol H, Pinho SS. Alterations in mucosa branched N-glycans lead to dysbiosis and downregulation of ILC3: a key driver of intestinal inflammation. Gut Microbes 2025; 17:2461210. [PMID: 39918275 PMCID: PMC11810091 DOI: 10.1080/19490976.2025.2461210] [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] [Received: 08/29/2024] [Revised: 11/29/2024] [Accepted: 01/13/2025] [Indexed: 02/12/2025] Open
Abstract
The perturbation of the symbiotic relationship between microbes and intestinal immune system contributes to gut inflammation and Inflammatory Bowel Disease (IBD) development. The host mucosa glycans (glycocalyx) creates a major biological interface between gut microorganisms and host immunity that remains ill-defined. Glycans are essential players in IBD immunopathogenesis, even years before disease onset. However, how changes in mucosa glycosylation shape microbiome and how this impact gut immune response and inflammation remains to be clarified. Here, we revealed that alterations in the expression of complex branched N-glycans at gut mucosa surface, modeled in glycoengineered mice, resulted in dysbiosis, with a deficiency in Firmicutes bacteria. Concomitantly, this mucosa N-glycan switch was associated with a downregulation of type 3 innate lymphoid cells (ILC3)-mediated immune response, leading to the transition of ILC3 toward an ILC1 proinflammatory phenotype and increased TNFα production. In addition, we demonstrated that the mucosa glycosylation remodeling through prophylactic supplementation with glycans at steady state was able to restore microbial-derived short-chain fatty acids and microbial sensing (by NOD2 expression) alongside the rescue of the expression of ILC3 module, suppressing intestinal inflammation and controlling disease onset. In a complementary approach, we further showed that IBD patients, often displaying dysbiosis, exhibited a tendency of decreased MGAT5 expression at epithelial cells that was accompanied by reduced ILC3 expression in gut mucosa. Altogether, these results unlock the effects of alterations in mucosa glycome composition in the regulation of the bidirectional crosstalk between microbiota and gut immune response, revealing host branched N-glycans/microbiota/ILC3 axis as an essential pathway in gut homeostasis and in preventing health to intestinal inflammation transition.
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Affiliation(s)
- Cláudia S. Rodrigues
- Institute for Research and Innovation in Health (i3S), Immunology, Cancer & Glycomedicine Group, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
| | - Joana Gaifem
- Institute for Research and Innovation in Health (i3S), Immunology, Cancer & Glycomedicine Group, University of Porto, Porto, Portugal
| | - Márcia S. Pereira
- Institute for Research and Innovation in Health (i3S), Immunology, Cancer & Glycomedicine Group, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
| | - Maria Francisca Alves
- Institute for Research and Innovation in Health (i3S), Immunology, Cancer & Glycomedicine Group, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - Mariana Silva
- Institute for Research and Innovation in Health (i3S), Immunology, Cancer & Glycomedicine Group, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
| | - Nuno Padrão
- Institute for Research and Innovation in Health (i3S), Immunology, Cancer & Glycomedicine Group, University of Porto, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Bruno Cavadas
- Institute for Research and Innovation in Health (i3S), Immunology, Cancer & Glycomedicine Group, University of Porto, Porto, Portugal
| | | | - Inês Alves
- Institute for Research and Innovation in Health (i3S), Immunology, Cancer & Glycomedicine Group, University of Porto, Porto, Portugal
| | - Ricardo Marcos-Pinto
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
- Department of Gastroenterology, Centro Hospitalar do Porto, Porto, Portugal
- Centro de Investigação em Tecnologias e Serviços de Saúde, University of Porto, Porto, Portugal
| | - Joana Torres
- Division of Gastroenterology, Hospital Beatriz Ângelo, Loures, Portugal
- Faculty of Medicine, University of Lisbon, Lisbon, Portugal
- Division of Gastroenterology, Hospital da Luz, Lisbon, Portugal
| | - Aonghus Lavelle
- Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint-Antoine Hospital, Gastroenterology Department, Sorbonne Université, INSERM, Paris, France
| | - Jean-Frederic Colombel
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Harry Sokol
- Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint-Antoine Hospital, Gastroenterology Department, Sorbonne Université, INSERM, Paris, France
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM) FHU, Paris, France
| | - Salomé S. Pinho
- Institute for Research and Innovation in Health (i3S), Immunology, Cancer & Glycomedicine Group, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
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16
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Li P, Ma W, Cheng J, Zhan C, Lu H, Shen J, Zhou X. Phages adapt to recognize an O-antigen polysaccharide site by mutating the "backup" tail protein ORF59, enabling reinfection of phage-resistant Klebsiella pneumoniae. Emerg Microbes Infect 2025; 14:2455592. [PMID: 39817558 PMCID: PMC11795761 DOI: 10.1080/22221751.2025.2455592] [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: 10/18/2024] [Revised: 12/10/2024] [Accepted: 01/14/2025] [Indexed: 01/18/2025]
Abstract
Phages demonstrate remarkable promise as antimicrobial agents against antibiotic-resistant bacteria. However, the emergence of phage-resistant strains poses challenges to their effective application. In this paper, we presented the isolation of a phage adaptive mutant that demonstrated enhanced and sustained antibacterial efficacy through the co-evolution of Klebsiella pneumoniae (K. pneumoniae) 111-2 and phage ZX1Δint in vitro. Our experiments revealed that phage ZX1Δint successfully completed the adsorption phase by binding to the host surface, specifically targeting the capsular polysaccharide (CPS) receptor via the primary receptor-binding protein (RBP) ORF60 and the auxiliary RBP ORF59. Upon exposure to phage predation, mutations in genes wbaP, wbaZ or wzc, which encode the synthesis of the CPS, conferred resistance by reducing phage adsorption. In response to these host defense mechanisms, the adaptive mutant phages have evolved to utilize an alternative binding site located on an O-antigen site of lipopolysaccharide (LPS) through a mutation in the backup RBP ORF59. This evolutionary change enabled the phages to reinfect previously phage-resistant strains. Notably, the adaptive mutant phage PR2 carrying the ORF59 mutation Q777R, demonstrated the capacity to infect both wild-type and resistant strains, exhibiting prolonged antimicrobial activity against the wild strains. In conclusion, our findings elucidated a complex phage-host adsorption-antagonism mechanism characterized by mutation-driven alterations in phage receptor recognition. This work contributes to a deeper understanding of phage adaptability and highlights the potential for phages to combat phage-resistant bacteria through an in vitro evolutionary approach.
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Affiliation(s)
- Ping Li
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou, People’s Republic of China
| | - Wenjie Ma
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou, People’s Republic of China
| | - Jun Cheng
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou, People’s Republic of China
| | - Cuixing Zhan
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou, People’s Republic of China
| | - Hongzhou Lu
- National Clinical Research Center, Shenzhen Third People’s Hospital, Shenzhen, People’s Republic of China
| | - Jiayin Shen
- National Clinical Research Center, Shenzhen Third People’s Hospital, Shenzhen, People’s Republic of China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, People’s Republic of China
| | - Xin Zhou
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, People’s Republic of China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou, People’s Republic of China
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17
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Forte G, Boteva L, Gilbert N, Cook PR, Marenduzzo D. Bridging-mediated compaction of mitotic chromosomes. Nucleus 2025; 16:2497765. [PMID: 40340634 PMCID: PMC12068332 DOI: 10.1080/19491034.2025.2497765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2025] [Revised: 03/27/2025] [Accepted: 04/21/2025] [Indexed: 05/10/2025] Open
Abstract
Within living cells, chromosome shapes undergo a striking morphological transition, from loose and uncondensed fibers during interphase to compacted and cylindrical structures during mitosis. ATP driven loop extrusion performed by a specialized protein complex, condensin, has recently emerged as a key driver of this transition. However, while this mechanism can successfully recapitulate the compaction of chromatids during the early stages of mitosis, it cannot capture structures observed after prophase. Here we hypothesize that a condensin bridging activity plays an additional important role, and review evidence - obtained largely through molecular dynamics simulations - that, in combination with loop extrusion, it can generate compact metaphase cylinders. Additionally, the resulting model qualitatively explains the unusual elastic properties of mitotic chromosomes observed in micromanipulation experiments and provides insights into the role of condensins in the formation of abnormal chromosome structures associated with common fragile sites.
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Affiliation(s)
- Giada Forte
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Lora Boteva
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Nick Gilbert
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Peter R. Cook
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Davide Marenduzzo
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
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18
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Meza-Torres J, Tinevez JY, Crouzols A, Mary H, Kim M, Hunault L, Chamorro-Rodriguez S, Lejal E, Altamirano-Silva P, Groussard D, Gobaa S, Peltier J, Chassaing B, Dupuy B. Clostridioides difficile binary toxin CDT induces biofilm-like persisting microcolonies. Gut Microbes 2025; 17:2444411. [PMID: 39719371 DOI: 10.1080/19490976.2024.2444411] [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] [Received: 07/19/2024] [Revised: 11/07/2024] [Accepted: 12/09/2024] [Indexed: 12/26/2024] Open
Abstract
Clinical symptoms of Clostridioides difficile infection (CDI) range from diarrhea to pseudomembranous colitis. A major challenge in managing CDI is the high rate of relapse. Several studies correlate the production of CDT binary toxin by clinical strains of C. difficile with higher relapse rates. Although the mechanism of action of CDT on host cells is known, its exact contribution to CDI is still unclear. To understand the physiological role of CDT during CDI, we established two hypoxic relevant intestinal models, Transwell and Microfluidic Intestine-on-Chip systems. Both were challenged with the epidemic strain UK1 CDT+ and its isogenic CDT- mutant. We report that CDT induces mucin-associated microcolonies that increase C. difficile colonization and display biofilm-like properties by enhancing C. difficile resistance to vancomycin. Importantly, biofilm-like microcolonies were also observed in the cecum and colon of infected mice. Hence, our study shows that CDT induces biofilm-like microcolonies, increasing C. difficile persistence and risk of relapse.
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Affiliation(s)
- Jazmin Meza-Torres
- Pathogenesis of Bacterial Anaerobes, Department of Microbiology, Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Paris, France
| | - Jean-Yves Tinevez
- Image Analysis Hub, Department of Cell Biology and Infection, Institut Pasteur, Université Paris Cité, Paris, France
| | - Aline Crouzols
- Pathogenesis of Bacterial Anaerobes, Department of Microbiology, Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Paris, France
| | - Héloïse Mary
- Biomaterials and Microfluidics Core Facility, Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, Paris, France
| | - Minhee Kim
- Biomaterials and Microfluidics Core Facility, Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, Paris, France
| | - Lise Hunault
- Antibodies in Therapy and Pathology, Department of Immunology, Institut Pasteur, Paris, France
| | - Susan Chamorro-Rodriguez
- Pathogenesis of Bacterial Anaerobes, Department of Microbiology, Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Paris, France
| | - Emilie Lejal
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Pamela Altamirano-Silva
- Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | | | - Samy Gobaa
- Biomaterials and Microfluidics Core Facility, Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, Paris, France
| | - Johann Peltier
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Benoit Chassaing
- Microbiome-Host Interactions, Department of Microbiology, Institut Pasteur, Université Paris Cité, INSERM U1306, Paris, France
- Mucosal Microbiota in Chronic Inflammatory Diseases, INSERM U1016, CNRS UMR 8104, Université Paris Cité, Paris, France
| | - Bruno Dupuy
- Pathogenesis of Bacterial Anaerobes, Department of Microbiology, Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Paris, France
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19
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Zhang M, Lu Z. tRNA modifications: greasing the wheels of translation and beyond. RNA Biol 2025; 22:1-25. [PMID: 39723662 DOI: 10.1080/15476286.2024.2442856] [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] [Revised: 11/29/2024] [Accepted: 12/11/2024] [Indexed: 12/28/2024] Open
Abstract
Transfer RNA (tRNA) is one of the most abundant RNA types in cells, acting as an adaptor to bridge the genetic information in mRNAs with the amino acid sequence in proteins. Both tRNAs and small fragments processed from them play many nonconventional roles in addition to translation. tRNA molecules undergo various types of chemical modifications to ensure the accuracy and efficiency of translation and regulate their diverse functions beyond translation. In this review, we discuss the biogenesis and molecular mechanisms of tRNA modifications, including major tRNA modifications, writer enzymes, and their dynamic regulation. We also summarize the state-of-the-art technologies for measuring tRNA modification, with a particular focus on 2'-O-methylation (Nm), and discuss their limitations and remaining challenges. Finally, we highlight recent discoveries linking dysregulation of tRNA modifications with genetic diseases.
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Affiliation(s)
- Minjie Zhang
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Medical Epigenetics, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhipeng Lu
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
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20
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Wang S, Li F, Feng X, Feng M, Niu X, Jiang X, Chen W, Bai R. Promoting collagen synthesis: a viable strategy to combat skin ageing. J Enzyme Inhib Med Chem 2025; 40:2488821. [PMID: 40213810 PMCID: PMC11995770 DOI: 10.1080/14756366.2025.2488821] [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: 01/20/2025] [Revised: 03/24/2025] [Accepted: 03/31/2025] [Indexed: 04/16/2025] Open
Abstract
Skin ageing is a complex physiological process primarily characterised by the deepening of wrinkles and the sagging of the skin. Collagen is essential for maintaining skin elasticity and firmness. As skin ages, it experiences structural and functional changes in collagen, including a decrease in collagen synthesis and an increase in collagen hydrolysis. Thus, promoting collagen synthesis represents a practical strategy for mitigating skin ageing. This review systematically described the functions, classifications and biosynthesis process of collagen, as well as its role in skin ageing. Additionally, the major signalling pathways and targets associated with collagen synthesis were also discussed. More importantly, the review provided a detailed summary of natural products with collagen synthesis-promoting effects and highlighted small molecule compounds with potential anti-ageing activity, especially PPARδ agonists. The relevant content offers potential targets and lead compounds for the development of anti-skin ageing therapies.
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Affiliation(s)
- Shan Wang
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, PR China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, PR China
| | - Feifan Li
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, PR China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, PR China
| | - Xilong Feng
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, PR China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, PR China
| | - Meiling Feng
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, PR China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, PR China
| | - Xiaotian Niu
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, PR China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, PR China
| | - Xiaoying Jiang
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, PR China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, PR China
| | - Wenchao Chen
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, PR China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, PR China
| | - Renren Bai
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, PR China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, PR China
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21
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Wu X, Xu H, Xia E, Gao L, Hou Y, Sun L, Zhang H, Cheng Y. Histone modifications in the regulation of erythropoiesis. Ann Med 2025; 57:2490824. [PMID: 40214280 PMCID: PMC11995772 DOI: 10.1080/07853890.2025.2490824] [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] [Received: 11/16/2024] [Revised: 03/13/2025] [Accepted: 04/01/2025] [Indexed: 04/16/2025] Open
Abstract
INTRODUCTION The pathogenesis of anemia and other erythroid dysphasia are mains poorly understood, primarily due to limited knowledge about the differentiation processes and regulatory mechanisms governing erythropoiesis. Erythropoiesis is a highly complex and precise biological process, that can be categorized into three distinct stages: early erythropoiesis, terminal erythroid differentiation, and reticulocyte maturation, and this complex process is tightly controlled by multiple regulatory factors. Emerging evidence highlights the crucial role of epigenetic modifications, particularly histone modifications, in regulating erythropoiesis. Methylation and acetylation are two common modification forms that affect genome accessibility by altering the state of chromatin, thereby regulating gene expression during erythropoiesis. DISCUSSION This review systematically examines the roles of histone methylation and acetylation, along with their respective regulatory enzymes, in regulating the development and differentiation of hematopoietic stem/progenitor cells (HSPCs) and erythroid progenitors. Furthermore, we discuss the involvement of these histone modifications in erythroid-specific developmental processes, including hemoglobin switching, chromatin condensation, and enucleation.Conclusions This review summarizes the current understanding of the role of histone modifications in erythropoiesis based on existing research, as a foundation for further research the mechanisms of epigenetic regulatory in erythropoiesis.
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Affiliation(s)
- Xiuyun Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Hongdi Xu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Erxi Xia
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Linru Gao
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Yan Hou
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Lei Sun
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Hengchao Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Ying Cheng
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
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22
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Yang M, Jiang Z, Zhou L, Chen N, He H, Li W, Yu Z, Jiao S, Song D, Wang Y, Jin M, Lu Z. 3'-Sialyllactose and B. infantis synergistically alleviate gut inflammation and barrier dysfunction by enriching cross-feeding bacteria for short-chain fatty acid biosynthesis. Gut Microbes 2025; 17:2486512. [PMID: 40195063 PMCID: PMC11988227 DOI: 10.1080/19490976.2025.2486512] [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] [Received: 12/17/2024] [Revised: 03/07/2025] [Accepted: 03/25/2025] [Indexed: 04/09/2025] Open
Abstract
Ulcerative colitis (UC) poses significant threats to human health and quality of life worldwide, as it is a chronic inflammatory bowel disease. 3'-sialyllactose (3'-SL) is a key functional component of milk oligosaccharides. This study systematically evaluates the prebiotic effects of 3'-SL and its therapeutic potential in combination with Bifidobacterium infantis (B. infantis) for UC. The findings reveal that 3'-SL and B. infantis synergistically mitigate intestinal inflammation and barrier dysfunction by promoting the production of short-chain fatty acids (SCFAs) through cross-feeding mechanisms among gut microbiota. Individually, 3'-SL, B. infantis, and the synbiotic treatment all effectively alleviated UC symptoms, including reduced weight loss, improved disease activity scores, and prevention of colon shortening. Histopathological and immunofluorescence analyses further demonstrated that the synbiotic treatment significantly ameliorated colonic injury, enhanced barrier function, restored goblet cell counts, increased glycoprotein content in crypt goblet cells, and upregulated the expression of tight junction proteins (ZO-1, occludin, and claudin-1). Notably, the synbiotic treatment outperformed the individual components by better restoring gut microbiota balance, elevating SCFA levels, and modulating serum cytokine profiles, thereby reducing inflammation. These findings provide mechanistic insights into the protective effects of the synbiotic and underscore its therapeutic potential for UC and other intestinal inflammatory disorders.
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Affiliation(s)
- Mingzhi Yang
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, China
- National Engineering Research Center of Green Feed and Healthy Breeding, Hangzhou, China
- Zhejiang Key Laboratory of Nutrition and Breeding for High-Quality Animal Products, Hangzhou, China
| | - Zipeng Jiang
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, China
- National Engineering Research Center of Green Feed and Healthy Breeding, Hangzhou, China
- Zhejiang Key Laboratory of Nutrition and Breeding for High-Quality Animal Products, Hangzhou, China
| | - Lutong Zhou
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, China
- National Engineering Research Center of Green Feed and Healthy Breeding, Hangzhou, China
- Zhejiang Key Laboratory of Nutrition and Breeding for High-Quality Animal Products, Hangzhou, China
| | - Nana Chen
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, China
- National Engineering Research Center of Green Feed and Healthy Breeding, Hangzhou, China
- Zhejiang Key Laboratory of Nutrition and Breeding for High-Quality Animal Products, Hangzhou, China
| | - Huan He
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, China
- National Engineering Research Center of Green Feed and Healthy Breeding, Hangzhou, China
- Zhejiang Key Laboratory of Nutrition and Breeding for High-Quality Animal Products, Hangzhou, China
| | - Wentao Li
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, China
- National Engineering Research Center of Green Feed and Healthy Breeding, Hangzhou, China
- Zhejiang Key Laboratory of Nutrition and Breeding for High-Quality Animal Products, Hangzhou, China
| | - Zhixin Yu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, China
- National Engineering Research Center of Green Feed and Healthy Breeding, Hangzhou, China
- Zhejiang Key Laboratory of Nutrition and Breeding for High-Quality Animal Products, Hangzhou, China
| | - Siming Jiao
- Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Deguang Song
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Yizhen Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, China
- National Engineering Research Center of Green Feed and Healthy Breeding, Hangzhou, China
- Zhejiang Key Laboratory of Nutrition and Breeding for High-Quality Animal Products, Hangzhou, China
| | - Mingliang Jin
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, China
- National Engineering Research Center of Green Feed and Healthy Breeding, Hangzhou, China
- Zhejiang Key Laboratory of Nutrition and Breeding for High-Quality Animal Products, Hangzhou, China
| | - Zeqing Lu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, China
- National Engineering Research Center of Green Feed and Healthy Breeding, Hangzhou, China
- Zhejiang Key Laboratory of Nutrition and Breeding for High-Quality Animal Products, Hangzhou, China
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23
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Loison L, Huré M, Lefranc B, Leprince J, Bôle-Feysot C, Coëffier M, Ribet D. Staphylococcus warneri dampens SUMOylation and promotes intestinal inflammation. Gut Microbes 2025; 17:2446392. [PMID: 39819277 DOI: 10.1080/19490976.2024.2446392] [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] [Received: 04/28/2024] [Revised: 11/28/2024] [Accepted: 12/18/2024] [Indexed: 01/19/2025] Open
Abstract
Gut bacteria play key roles in intestinal physiology, via the secretion of diversified bacterial effectors. Many of these effectors remodel the host proteome, either by altering transcription or by regulating protein post-translational modifications. SUMOylation, a ubiquitin-like post-translational modification playing key roles in intestinal physiology, is a target of gut bacteria. Mutualistic gut bacteria can promote SUMOylation, via the production of short- or branched-chain fatty acids (SCFA/BCFA). In contrast, several pathogenic bacteria were shown to dampen SUMOylation in order to promote infection. Here, we demonstrate that Staphylococcus warneri, a natural member of the human gut microbiota, decreases SUMOylation in intestinal cells. We identify that Warnericin RK, a hemolytic toxin secreted by S. warneri, targets key components of the host SUMOylation machinery, leading to the loss of SUMO-conjugated proteins. We further demonstrate that Warnericin RK promotes inflammation in intestinal and immune cells using both SUMO-dependent and SUMO-independent mechanisms. We finally show that Warnericin RK regulates the expression of genes involved in intestinal tight junctions. Together, these results highlight the diversity of mechanisms used by bacteria from the gut microbiota to manipulate host SUMOylation. They further highlight that changes in gut microbiota composition may impact intestinal inflammation, by altering the equilibrium between bacterial effectors promoting or dampening SUMOylation.
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Affiliation(s)
- Léa Loison
- Univ Rouen Normandie, INSERM, Normandie Univ, ADEN, UMR 1073 Nutrition, Inflammation and Microbiota-Gut-Brain axis, Rouen, France
| | - Marion Huré
- Univ Rouen Normandie, INSERM, Normandie Univ, ADEN, UMR 1073 Nutrition, Inflammation and Microbiota-Gut-Brain axis, Rouen, France
| | - Benjamin Lefranc
- Univ Rouen Normandie, INSERM, Normandie Univ, NorDiC, UMR 1239, PRIMACEN, Rouen, France
| | - Jérôme Leprince
- Univ Rouen Normandie, INSERM, Normandie Univ, NorDiC, UMR 1239, PRIMACEN, Rouen, France
| | - Christine Bôle-Feysot
- Univ Rouen Normandie, INSERM, Normandie Univ, ADEN, UMR 1073 Nutrition, Inflammation and Microbiota-Gut-Brain axis, Rouen, France
| | - Moïse Coëffier
- Univ Rouen Normandie, INSERM, Normandie Univ, ADEN, UMR 1073 Nutrition, Inflammation and Microbiota-Gut-Brain axis, CHU Rouen, Department of Nutrition, CIC-CRB1404, Rouen, France
| | - David Ribet
- Univ Rouen Normandie, INSERM, Normandie Univ, ADEN, UMR 1073 Nutrition, Inflammation and Microbiota-Gut-Brain axis, Rouen, France
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24
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Cheng Z, Sun Y, Shen Y, Wu X, Pan L, Wu H, Bai Y, Zhao C, Ma J, Huang W. A single mutation at position 214 of influenza B hemagglutinin enhances cross-neutralization. Emerg Microbes Infect 2025; 14:2467770. [PMID: 39960410 PMCID: PMC11849025 DOI: 10.1080/22221751.2025.2467770] [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: 11/04/2024] [Revised: 02/09/2025] [Accepted: 02/11/2025] [Indexed: 02/22/2025]
Abstract
High variability of influenza B virus (IBV) hemagglutinin (HA) impairs the cross- neutralization ability of vaccines, leading to reduce efficacy. We identified significant differences in cross-neutralization between IBV strains B/Wyoming/06/2014 and B/Brisbane/60/2008, which differ in only three amino acid residues. The 214 T point mutation was found to dramatically enhance cross-neutralization (>10-fold). Antibody-based reverse validation also revealed that this mutation significantly increased the neutralization capacity (500-62,500-fold). Furthermore, monitoring revealed that the mutation rate at this site has reached its highest level in nearly 20 years, with a prevalence exceeding 80% in sequences submitted from certain regions. Our findings provide new evidence for the selection of vaccine strains with improved cross- neutralization effects, which will aid the development of broad-spectrum vaccines by modifying minimal antigenic epitopes.
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Affiliation(s)
- Ziqi Cheng
- National Engineering Laboratory for AIDS Vaccines, School of Life Sciences, Jilin University, Changchun, People’s Republic of China
- Division of HIV/AIDS and Sexually transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, People’s Republic of China
| | - Yeqing Sun
- National Engineering Laboratory for AIDS Vaccines, School of Life Sciences, Jilin University, Changchun, People’s Republic of China
- Division of HIV/AIDS and Sexually transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, People’s Republic of China
| | - Yanru Shen
- Division of HIV/AIDS and Sexually transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, People’s Republic of China
| | - Xi Wu
- Division of HIV/AIDS and Sexually transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, People’s Republic of China
| | - Ling Pan
- Division of HIV/AIDS and Sexually transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, People’s Republic of China
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, People’s Republic of China
| | - Hao Wu
- Division of HIV/AIDS and Sexually transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, People’s Republic of China
| | - Yunbo Bai
- Division of HIV/AIDS and Sexually transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, People’s Republic of China
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, People’s Republic of China
| | - Chenyan Zhao
- Division of HIV/AIDS and Sexually transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, People’s Republic of China
| | - Junfeng Ma
- National Engineering Laboratory for AIDS Vaccines, School of Life Sciences, Jilin University, Changchun, People’s Republic of China
| | - Weijin Huang
- Division of HIV/AIDS and Sexually transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, People’s Republic of China
- Graduate School of Peking Union Medical College, Beijing, People’s Republic of China
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25
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Chen X, Qin Y, Gan J, Wei T, Wei X, Xiong Y, Zhang Z, Wei B. Uncovering global research frontiers in deubiquitinating enzymes and immunotherapy: A bibliometric study. Hum Vaccin Immunother 2025; 21:2483558. [PMID: 40130728 PMCID: PMC11938311 DOI: 10.1080/21645515.2025.2483558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2024] [Revised: 02/28/2025] [Accepted: 03/15/2025] [Indexed: 03/26/2025] Open
Abstract
Recently, immunotherapy has been a key therapeutic strategy for cancer. Deubiquitinating enzymes (DUBs), which are protein-modifying enzymes, have a crucial role in the pathogenesis of cancer, autoimmune diseases, and inflammation. DUBs influence the tumor immune microenvironment by regulating immune cell functions and key signaling pathways. Thus, the potential applications of DUBs in immunotherapy have piqued the interest of the scientific community. This study performed bibliometric analysis to comprehensively examine the research hotspots and trends in this field, providing theoretical foundations and guidance for future research. Studies associated with DUBs and immunotherapy conducted over a decade (2014 to 2024) were searched and extracted from Web of Science Collection database. The analysis was performed using CiteSpace, VOSviewer, and the Bibliometrix package in R software. Visualizations were generated for countries, institutions, authors, journals, references, and keyword co-occurrences. In total, 321 articles related to DUBs and immunotherapy were retrieved. The number of publications increased markedly since 2020. China had the highest number of publications, while the United States exerted the most influence in this field. Zhang Jinfang was the most influential author in this field. Zhejiang University was the institution with the highest number of publications. Nature was the most cited journal (807 total citations). Keyword analysis revealed that the primary research hotspots were expression, immunotherapy, ubiquitination, degradation, and cancer. This bibliometric analysis revealed the research trends and emerging frontiers in DUBs and immunotherapy, offering novel strategies for the application of DUBs in immunotherapy.
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Affiliation(s)
- Xia Chen
- Department of Geriatrics, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Yang Qin
- Department of Rheumatology and immunology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Jinfeng Gan
- Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, China
- Guangxi Health Commission Key Laboratory of Tumor Immunology and Receptor‑Targeted Drug Basic Research, Guilin Medical University, Guilin, China
| | - Tangwen Wei
- School of Public Health, Guilin Medical University, Guilin, China
| | - Xinyi Wei
- School of Public Health, Guangxi Medical University, Nanning, China
| | - Yaling Xiong
- Department of Gastrointestinal Surgery, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Zhichang Zhang
- Department of Computer, School of Intelligent Medicine China Medical University, Shenyang, Liaoning Province, China
| | - Bing Wei
- Department of Geriatrics, Affiliated Hospital of Guilin Medical University, Guilin, China
- Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin Medical University, Guilin, China
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26
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Santoro AM, Persico M, D’Urso A, Cunsolo A, Tkachuk O, Milardi D, Purrello R, Tundo GR, Sbardella D, Osmulski PA, Gaczynska M, Coletta M, Fattorusso C. Tetra-anionic porphyrin mimics protein-protein interactions between regulatory particles and the catalytic core, allosterically activating human 20S proteasome. J Enzyme Inhib Med Chem 2025; 40:2482892. [PMID: 40192126 PMCID: PMC11980194 DOI: 10.1080/14756366.2025.2482892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Revised: 03/03/2025] [Accepted: 03/11/2025] [Indexed: 04/11/2025] Open
Abstract
Decreased proteasome activity is a hallmark of brain and retinal neurodegenerative diseases (Alzheimer's, Parkinson's diseases, glaucoma) boosting the search for molecules acting as proteasome activators. Based on the hypothesis of an electrostatic key code driving catalytic core particle (20S) activation by regulatory particles (RPs), we identified the tetra-anionic meso-Tetrakis(4-sulphonatophenyl)-porphyrin (H2TPPS) as a new activator of human proteasome. By means of an integrated approach, including bioinformatics, enzymatic kinetic analysis, atomic force microscopy, and dynamic docking simulations, we show how binding of H2TPPS affects the closed/open conformational equilibrium of human 20S to ultimately promote substrate gate opening and proteolytic activity. These outcomes support our hypothesis and pave the way to the rational discovery of new proteasome allosteric modulators able to reproduce the key structural elements of regulatory particles responsible for catalytic activation.
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Affiliation(s)
- A. M. Santoro
- National Research Council, Institute of Crystallography, Sede Secondaria di Catania, Catania, Italy
| | - M. Persico
- Department of Pharmacy, University of Naples “Federico II”, Napoli, Italy
| | - A. D’Urso
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - A. Cunsolo
- Department of Chemical Sciences, University of Catania, Catania, Italy
- Epic Sciences, San Diego, California, USA
| | - O. Tkachuk
- Department of Pharmacy, University of Naples “Federico II”, Napoli, Italy
| | - D. Milardi
- National Research Council, Institute of Crystallography, Sede Secondaria di Catania, Catania, Italy
| | - R. Purrello
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - G. R. Tundo
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy
| | | | - P. A. Osmulski
- Department of Molecular Medicine, University of Texas Health at San Antonio, San Antonio, Texas, USA
| | - M. Gaczynska
- Department of Molecular Medicine, University of Texas Health at San Antonio, San Antonio, Texas, USA
| | | | - C. Fattorusso
- Department of Pharmacy, University of Naples “Federico II”, Napoli, Italy
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27
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Lee JS, Kao DJ, Worledge CS, Villamaria ZF, Wang RX, Welch NM, Kostelecky RE, Colgan SP. E. coli genetically modified for purine nucleobase release promotes butyrate generation and colonic wound healing during DSS insult. Gut Microbes 2025; 17:2490211. [PMID: 40247632 PMCID: PMC12013446 DOI: 10.1080/19490976.2025.2490211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 12/27/2024] [Accepted: 04/03/2025] [Indexed: 04/19/2025] Open
Abstract
The gut microbiota transforms energy stored as undigestible carbohydrates into a remarkable number of metabolites that fuel intestinal bacterial communities and the host tissue. Colonic epithelial cells at the microbiota-host interface depend upon such microbiota-derived metabolites (MDMs) to satisfy their energy requisite. Microbial dysbiosis eliciting MDM loss contributes to barrier dysfunction and mucosal disease. Recent work has identified a role for microbiota-sourced purines (MSPs), notably hypoxanthine, as an MDM salvaged by the colonic epithelium for nucleotide biogenesis and energy balance. Here, we investigated the role of MSPs in mice during disease-modeled colonic energetic stress using a strain of E. coli genetically modified for enhanced purine nucleobase release (E. coli Mutant). E. coli Mutant colonization protected against DSS-induced tissue damage and permeability while promoting proliferation for wound healing. Metabolite and metagenomic analyses suggested a colonic butyrate-purine nucleobase metabolic axis, wherein the E. coli Mutant provided purine substrate for Clostridia butyrate production and host purine salvage, altogether supplying the host substrate for efficient nucleotide biogenesis and energy balance.
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Affiliation(s)
- J. Scott Lee
- Department of Medicine, Mucosal Inflammation Program, University of Colorado Anschutz Medical Campus
| | - Daniel J. Kao
- Department of Medicine, Mucosal Inflammation Program, University of Colorado Anschutz Medical Campus
| | - Corey S. Worledge
- Department of Medicine, Mucosal Inflammation Program, University of Colorado Anschutz Medical Campus
| | - Zachary F. Villamaria
- Department of Medicine, Mucosal Inflammation Program, University of Colorado Anschutz Medical Campus
| | - Ruth X. Wang
- Department of Medicine, Mucosal Inflammation Program, University of Colorado Anschutz Medical Campus
| | - Nichole M. Welch
- Department of Medicine, Mucosal Inflammation Program, University of Colorado Anschutz Medical Campus
- Department of Medicine, Rocky Mountain Veterans Association, Aurora, CO, USA
| | - Rachael E. Kostelecky
- Department of Medicine, Mucosal Inflammation Program, University of Colorado Anschutz Medical Campus
| | - Sean P. Colgan
- Department of Medicine, Mucosal Inflammation Program, University of Colorado Anschutz Medical Campus
- Department of Medicine, Rocky Mountain Veterans Association, Aurora, CO, USA
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28
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Chagraoui A, Thibaut F, De Deurwaerdère P. 5-HT6 receptors: Contemporary views on their neurobiological and pharmacological relevance in neuropsychiatric disorders. DIALOGUES IN CLINICAL NEUROSCIENCE 2025; 27:112-128. [PMID: 40347153 PMCID: PMC12068339 DOI: 10.1080/19585969.2025.2502028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Revised: 04/02/2025] [Accepted: 04/30/2025] [Indexed: 05/12/2025]
Abstract
Despite the relatively limited number of serotonergic neurons in humans, serotonin plays a key role in neurophysiological functions, including sleep, pain perception, learning, memory, cognition, emotion, reward, and mood regulation. Altered serotonergic neurotransmission is linked to conditions such as anxiety, depression, anorexia, migraine, insomnia, schizophrenia, Alzheimer's disease (AD), and cognitive impairments. The 5-HT6 receptor (5-HT6R), mainly found in brain regions involved in cognition, is a promising therapeutic target for cognitive deficits in neuropsychiatric disorders, particularly AD and schizophrenia. Preclinical studies have shown that 5-HT6R antagonists improve cognitive function. 5-HT6R interacts dynamically with an extensive intracellular protein network, regulating the localisation, trafficking, and signalling of these proteins. Proteomic and genetic studies have revealed interactions with mTOR kinase and neurofibromin, both of which are crucial for synaptic plasticity, learning, and memory. Fyn kinase is also associated with 5-HT6Rs, reinforcing receptor expression and G-protein coupling. Notably, the G protein-regulated inducer of neurite outgrowth 1 (GPRIN1) interacts with 5-HT6Rs independently of agonists, enhancing receptor activity. This review highlights the clinical testing of 5-HT6R ligands as regulators of these complex signalling properties, underscoring their therapeutic potential in addressing cognitive impairments associated with neuropsychiatric disorders.
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Affiliation(s)
- Abdeslam Chagraoui
- Department of Medical Biochemistry, Rouen University Hospital, CHU de Rouen, France
- University of Rouen, Faculty of Medicine and Pharmacy, Inserm U1239, Neuroendocrine, Endocrine, and Germinal Differentiation and Communication (NorDiC), Mont-Saint-Aignan, France
| | - Florence Thibaut
- Department of Psychiatry and Addictive Disorders, University Hospital Cochin (site Tarnier) AP-HP, Paris, France
- INSERM U1266, Institute of Psychiatry and Neurosciences, University of Paris, Cité, Paris, France
| | - Philippe De Deurwaerdère
- Centre National de la Recherche Scientifique, Institut des Neurosciences Intégratives et Cognitives d’Aquitaine, UMR 5287, Bordeaux, France
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Sun J, Liu C, Yang G, Li Q, An Y, Zhu Y, Zhang P, Guan Y, Peng C, Du Z, Huang P, Chen Y. Targeting NEDD8 in pediatric acute myeloid leukemia: an integrated bioinformatics and experimental approach. Hematology 2025; 30:2478650. [PMID: 40103351 DOI: 10.1080/16078454.2025.2478650] [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: 08/21/2024] [Accepted: 03/06/2025] [Indexed: 03/20/2025] Open
Abstract
SUMMARYThis study systematically explored the role of NEDD8 in pediatric acute myeloid leukemia (AML) through patient sample analysis, database mining, and in vitro experiments. Our results demonstrated that NEDD8 was significantly overexpressed in newly diagnosed pediatric AML patients and was associated with poor survival outcomes. Functional enrichment analysis of the TARGET database further revealed a strong correlation between NEDD8 and cancer-related pathways. In vitro experiments showed that NEDD8 knockdown significantly inhibited the proliferation of AML cells (THP-1 and MV4-11) and induced cell cycle arrest. Collectively, these findings highlight the critical role of NEDD8 in pediatric AML pathogenesis and suggest its potential as both a prognostic biomarker and a therapeutic target.
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MESH Headings
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/pathology
- NEDD8 Protein/genetics
- NEDD8 Protein/metabolism
- Child
- Computational Biology/methods
- Female
- Male
- Cell Line, Tumor
- Child, Preschool
- Cell Proliferation
- Gene Expression Regulation, Leukemic
- Prognosis
- Adolescent
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Affiliation(s)
- Jian Sun
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, People's Republic of China
- Department of Hematological Oncology and Immunology, Guizhou Children's Hospital, Zunyi, People's Republic of China
| | - Cui Liu
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, People's Republic of China
- Department of Hematological Oncology and Immunology, Guizhou Children's Hospital, Zunyi, People's Republic of China
| | - Guangli Yang
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, People's Republic of China
- Department of Hematological Oncology and Immunology, Guizhou Children's Hospital, Zunyi, People's Republic of China
| | - Qian Li
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, People's Republic of China
- Department of Hematological Oncology and Immunology, Guizhou Children's Hospital, Zunyi, People's Republic of China
| | - Yang An
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, People's Republic of China
- Department of Hematological Oncology and Immunology, Guizhou Children's Hospital, Zunyi, People's Republic of China
| | - Yin Zhu
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, People's Republic of China
- Department of Hematological Oncology and Immunology, Guizhou Children's Hospital, Zunyi, People's Republic of China
| | - Pingping Zhang
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, People's Republic of China
- Department of Hematological Oncology and Immunology, Guizhou Children's Hospital, Zunyi, People's Republic of China
| | - Yaning Guan
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, People's Republic of China
- Department of Hematological Oncology and Immunology, Guizhou Children's Hospital, Zunyi, People's Republic of China
| | - Chang Peng
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, People's Republic of China
- Department of Hematological Oncology and Immunology, Guizhou Children's Hospital, Zunyi, People's Republic of China
| | - Zuochen Du
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, People's Republic of China
- Department of Hematological Oncology and Immunology, Guizhou Children's Hospital, Zunyi, People's Republic of China
| | - Pei Huang
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, People's Republic of China
- Department of Hematological Oncology and Immunology, Guizhou Children's Hospital, Zunyi, People's Republic of China
| | - Yan Chen
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, People's Republic of China
- Department of Hematological Oncology and Immunology, Guizhou Children's Hospital, Zunyi, People's Republic of China
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Chen Y, Liu X, Zhou Y, Zheng Y, Xiao Y, Yuan X, Yan Q, Chen X. Functional characterization of four soybean C2H2 zinc-finger genes in Phytophthora resistance. PLANT SIGNALING & BEHAVIOR 2025; 20:2481185. [PMID: 40110654 PMCID: PMC11926910 DOI: 10.1080/15592324.2025.2481185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2024] [Revised: 03/08/2025] [Accepted: 03/13/2025] [Indexed: 03/22/2025]
Abstract
Soybean (Glycine max) is one of the most important industrial and oilseed crops; however, the yield is threatened by the invasion of various pathogens. Soybean stem and root rot, caused by Phytophthora sojae, is a destructive disease that significantly damages soybean production worldwide. C2H2 zinc finger protein (C2H2-ZFP) is a large transcription factor family in plants that plays crucial roles in stress response and hormone signal transduction. Given its importance, we analyzed the expression patterns of C2H2-ZFP family genes in response to P. sojae infection and selected four candidate genes to explore their molecular characteristics and functions related to P. sojae resistance. Subcellular localization analysis indicated that three ZFPs (GmZFP2, GmZFP3, and GmZFP4) were localized in the nucleus, while GmZFP1 was found in both the nucleus and plasma membrane. Dual-luciferase transient expression analysis revealed that all four ZFPs possessed transcriptional repression activation. Further transient expression in N. benthamiana leaves demonstrated that GmZFP2 induced significant cell death and reactive oxygen species (ROS) accumulation. GmZFP2 significantly enhanced the resistance to Phytophthora pathogens in N. benthamiana leaves and soybean hairy roots. This study provides insights in to the functional characterization of soybean ZFPs in Phytophthora resistance and demonstrates that GmZFP2 plays a positive role in P. sojae resistance in soybeans.
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Affiliation(s)
- Yuting Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xinyue Liu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yanyan Zhou
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yu Zheng
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Yating Xiao
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xingxing Yuan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Qiang Yan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
- School of Life Sciences, Jiangsu University, Zhenjiang, China
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Chen L, Wu Y, Lv T, Tuo R, Xiao Y. Mesenchymal stem cells enchanced by salidroside to inhibit ferroptosis and improve premature ovarian insufficiency via Keap1/Nrf2/GPX4 signaling. Redox Rep 2025; 30:2455914. [PMID: 39874130 PMCID: PMC11776066 DOI: 10.1080/13510002.2025.2455914] [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] [Indexed: 01/30/2025] Open
Abstract
BACKGROUND Regenerative medicine researches have shown that mesenchymal stem cells (MSCs) may be an effective treatment method for premature ovarian insufficiency (POI). However, the efficacy of MSCs is still limited. PURPOSE This study aims to explain whether salidroside and MSCs combination is a therapeutic strategy to POI and to explore salidroside-enhanced MSCs inhibiting ferroptosis via Keap1/Nrf2/GPX4 signaling. METHODS The effect of salidroside and MSCs on ovarian granular cells (GCs) was analyzed. After treatment, hormone levels and -fertility of rats were measured. Lipid peroxidation levels, iron deposition and mitochondrial morphology were detected. The genes and proteins of Keap1/Nrf2/GPX4 signaling were examined. RESULTS Salidroside and MSCs were found to inhibit cell death of GCs by reducing peroxidation and intracellular ferrous. Salidroside promotes the proliferation of MSCs and supports cell survival in ovary. Salidroside combined with MSCs therapy restored ovarian function, which was better than MSCs monotherapy. Salidroside-enhanced MSCs to inhibit ferroptosis. The results showed activation of the Keap1/Nrf2/GPX4 signaling and an increase in anti-ferroptosis molecule. CONCLUSIONS Salidroside-enhanced MSCs as a ferroptosis inhibitor and provide new therapeutic strategies for POI. The possible mechanisms of MSCs were related to maintaining redox homeostasis via a Keap1/Nrf2/GPX4 signaling.
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Affiliation(s)
- Lixuan Chen
- Department of Hematology, Shenzhen Qianhai Shekou Pilot Free Trade Zone Hospital, Shenzhen, People’s Republic of China
| | - Yingnan Wu
- Translational Medicine Center, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Tiying Lv
- Guangzhou University of Chinese Medicine, Guangzhou, People’s Republic of China
| | - Rui Tuo
- Guangzhou University of Chinese Medicine, Guangzhou, People’s Republic of China
| | - Yang Xiao
- Department of Hematology, Shenzhen Qianhai Shekou Pilot Free Trade Zone Hospital, Shenzhen, People’s Republic of China
- Guangzhou University of Chinese Medicine, Guangzhou, People’s Republic of China
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Jungfleisch J, Gebauer F. RNA-binding proteins as therapeutic targets in cancer. RNA Biol 2025; 22:1-8. [PMID: 40016176 PMCID: PMC11869776 DOI: 10.1080/15476286.2025.2470511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/04/2025] [Accepted: 02/17/2025] [Indexed: 03/01/2025] Open
Abstract
RNA-binding proteins (RBPs) have emerged as critical regulators of cancer progression, influencing virtually all hallmarks of cancer. Their ability to modulate gene expression patterns that promote or inhibit tumorigenesis has positioned RBPs as promising targets for novel anti-cancer therapies. This mini-review summarizes the current state of RBP-targeted cancer treatments, focusing on five examples, eIF4F, FTO, SF3B1, RBM39 and nucleolin. We highlight the diversity of current targeting approaches and discuss ongoing challenges including the complexity of RBP regulatory networks, potential off-target effects and the need for more specific targeting methods. By assessing the future potential of novel therapeutic avenues, we provide insights into the evolving landscape of cancer treatment and the critical role RBPs may play in next-generation therapeutics.
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Affiliation(s)
- Jennifer Jungfleisch
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Fátima Gebauer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
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33
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Rayêe D, Meier UT, Eliscovich C, Cvekl A. Nucleolar ribosomal RNA synthesis continues in differentiating lens fiber cells until abrupt nuclear degradation required for ocular lens transparency. RNA Biol 2025; 22:1-16. [PMID: 40126102 PMCID: PMC11959900 DOI: 10.1080/15476286.2025.2483118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Revised: 02/20/2025] [Accepted: 03/07/2025] [Indexed: 03/25/2025] Open
Abstract
Cellular differentiation requires highly coordinated action of all three transcriptional systems to produce rRNAs, mRNAs and various 'short' and 'long' non-coding RNAs by RNA Polymerase I, II and III systems, respectively. RNA Polymerase I catalyzes transcription of about 400 copies of mammalian rDNA genes, generating 18S, 5.8S and 28S rRNA molecules. Lens fiber cell differentiation is a unique process to study transcriptional mechanisms of individual crystallin genes as their very high transcriptional outputs are directly comparable only to globin genes in erythrocytes. Importantly, both terminally differentiated lens fiber cells and mammalian erythrocytes degrade their nuclei through different mechanisms. In lens, the generation of the organelle-free zone (OFZ) includes the degradation of mitochondria, endoplasmic reticulum, Golgi apparatus and nuclei. Here, using RNA fluorescence in situ hybridization (FISH), we evaluated nascent rRNA transcription, located in the nucleoli, during the process of mouse lens fiber cell differentiation. Lens fiber cell nuclei undergo morphological changes including chromatin condensation prior to their denucleation. Remarkably, nascent rRNA transcription persists in all nuclei that are in direct proximity of the OFZ. Additionally, changes in both nuclei and nucleoli shape were evaluated via immunofluorescence detection of fibrillarin, nucleolin, UBF and other proteins. These studies demonstrate for the first time that highly condensed lens fiber cell nuclei have the capacity to support nascent rRNA transcription. Thus, we propose that 'late' production of rRNA molecules and consequently of ribosomes increases crystallin protein synthesis machinery within the mature lens fibers.
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Affiliation(s)
- Danielle Rayêe
- Departments of Ophthalmology and Visual Sciences and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - U. Thomas Meier
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Carolina Eliscovich
- Departments of Medicine (Hepatology) and Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Aleš Cvekl
- Departments of Ophthalmology and Visual Sciences and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
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Sharma R, Mishra A, Bhardwaj M, Singh G, Indira Harahap LV, Vanjani S, Pan CH, Nepali K. Medicinal chemistry breakthroughs on ATM, ATR, and DNA-PK inhibitors as prospective cancer therapeutics. J Enzyme Inhib Med Chem 2025; 40:2489720. [PMID: 40256842 PMCID: PMC12013171 DOI: 10.1080/14756366.2025.2489720] [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: 01/14/2025] [Revised: 03/28/2025] [Accepted: 04/01/2025] [Indexed: 04/22/2025] Open
Abstract
This review discusses the critical roles of Ataxia Telangiectasia Mutated Kinase (ATM), ATM and Rad3-related Kinase (ATR), and DNA-dependent protein kinase (DNA-PK) in the DNA damage response (DDR) and their implications in cancer. Emphasis is placed on the intricate interplay between these kinases, highlighting their collaborative and distinct roles in maintaining genomic integrity and promoting tumour development under dysregulated conditions. Furthermore, the review covers ongoing clinical trials, patent literature, and medicinal chemistry campaigns on ATM/ATR/DNA-PK inhibitors as antitumor agents. Notably, the medicinal chemistry campaigns employed robust drug design strategies and aimed at assembling new structural templates with amplified DDR kinase inhibitory ability, as well as outwitting the pharmacokinetic liabilities of the existing DDR kinase inhibitors. Given the success attained through such endeavours, the clinical pipeline of DNA repair kinase inhibitors is anticipated to be supplemented by a reasonable number of tractable entries (DDR kinase inhibitors) soon.
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Affiliation(s)
- Ram Sharma
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Anshul Mishra
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Monika Bhardwaj
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Gurpreet Singh
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, India
| | | | - Sakshi Vanjani
- Molecular Medicine, University of South Florida, Tampa, FL, USA
| | - Chun Hsu Pan
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Kunal Nepali
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
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35
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Alayoubi AM, Ijaz A, Wali A, Hashmi JA, Alharbi A, Basit S. Zellweger syndrome; identification of mutations in PEX19 and PEX26 gene in Saudi families. Ann Med 2025; 57:2447400. [PMID: 39757991 PMCID: PMC11705544 DOI: 10.1080/07853890.2024.2447400] [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] [Received: 02/05/2024] [Revised: 03/23/2024] [Accepted: 12/02/2024] [Indexed: 01/07/2025] Open
Abstract
BACKGROUND Peroxisome biogenesis disorders (PBD) affect multiple organ systems. It is characterized by neurological dysfunction, hypotonia, ocular anomalies, craniofacial abnormalities, and absence of peroxisomes in fibroblasts. PBDs are associated with mutations in any of fourteen different PEX genes, which are involved in peroxisome biogenesis. Zellweger spectrum disorder (ZSD) is a severe form of PBD. More than 90% of the ZSD cases have mutations in PEX1, PEX6, PEX10, PEX12, and PEX26. Mutations in the PEX19 gene are rarely associated with PBD/ZSD; however, a large proportion of PEX26 mutations are associated with ZSD. METHODS We recruited two Saudi families with multiple affected individuals with dysmorphic features, including hypertelorism, large open fontanelles, generalized hypotonia, and epicanthal folds with poor reflexes since birth. Whole exome sequencing (WES) and Sanger sequencing was performed to identify the genetic cause. The frequency and pathogenicity of the identified mutations were assessed using various online bioinformatics tools. RESULTS WES identified a novel nonsense variant (c.367C > T) in the PEX19 gene in family A patients. This nonsense mutation was predicted to cause premature termination (p.Gln123*). A previously reported synonymous variant (c.228C > T; p.Gly76Gly) in PEX26 was found in a patient from family B. Both variants were segregating in an autosomal recessive manner in the respective families. CONCLUSION The present study has added a novel nonsense mutation to the mutation spectrum of PEX19, which is the second null mutation identified to date. Moreover, in this study, the importance of a synonymous exonic variant of PEX26 close to the splice donor site was explored in relation to pre-mRNA splicing and resulting disease manifestations.
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Affiliation(s)
- Abdulfatah M. Alayoubi
- Department of Basic Medical Sciences, College of Medicine & Center for Genetics and Inherited Diseases, Taibah University Medina, Medina, Saudi Arabia
| | - Ambreen Ijaz
- Department of Zoology, Sardar Bahadur Khan Women’s University Quetta, Quetta, Pakistan
| | - Abdul Wali
- Department of Biotechnology, Faculty of Life Sciences & Informatics, BUITEMS, Quetta, Pakistan
| | - Jamil A. Hashmi
- Department of Basic Medical Sciences, College of Medicine & Center for Genetics and Inherited Diseases, Taibah University Medina, Medina, Saudi Arabia
| | - Azizah Alharbi
- Department of Pediatrics, Medina Maternity and Children Hospital, King Salman bin Abdul Aziz Medical City, Medina, Saudi Arabia
| | - Sulman Basit
- Department of Basic Medical Sciences, College of Medicine & Center for Genetics and Inherited Diseases, Taibah University Medina, Medina, Saudi Arabia
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Toivanen K, De Sutter L, Wozniak A, Wyns K, Merikoski N, Salmikangas S, Duan J, Maksimow M, Lahtinen M, Böhling T, Schöffski P, Sihto H. Pharmacokinetic profile and in vivo anticancer efficacy of anagrelide administered subcutaneously in rodents. Drug Deliv 2025; 32:2463433. [PMID: 39930717 PMCID: PMC11816618 DOI: 10.1080/10717544.2025.2463433] [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: 07/31/2024] [Revised: 12/18/2024] [Accepted: 01/31/2025] [Indexed: 02/14/2025] Open
Abstract
Anagrelide (ANA) is a phosphodiesterase 3A (PDE3A) inhibitor, commonly prescribed for essential thrombocythemia. It also functions as a molecular glue, inducing complex formation between PDE3A and Schlafen 12. This association either triggers apoptosis or inhibits proliferation in tumor cells, supporting its use in cancer therapy. Conventionally administered orally, ANA undergoes rapid metabolism and elimination, resulting in a short drug exposure time at the site of action. Here, we explored the pharmacokinetic profile of a subcutaneously (SC) injected ANA formulation in Sprague-Dawley rats by quantifying plasma ANA and metabolite concentrations using liquid-chromatography-tandem mass spectrometry. We further evaluated the in vivo tumor regression efficacy of orally and SC administered ANA in a patient-derived gastrointestinal stromal xenograft mouse model - UZLX-GIST2B - characterized by a KIT exon 9 driver mutation. The SC ANA exhibited extended-release plasma concentration-time profiles compared to intravenous and oral administrations. After a single administration in rats, plasma concentrations of ANA were detected up to 56 days later, and ANA metabolites up to 30 days later. The SC formulation also significantly reduced tumor volumes and demonstrated dose-dependent histological responses, nearly eradicating tumor tissue in 11 days with the highest dose. These findings suggest that the SC slow-release formulation maintains stable drug concentrations during treatment, potentially improving therapeutic efficacy at the target site.
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Affiliation(s)
- Kirsi Toivanen
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Luna De Sutter
- Department of Oncology, Laboratory of Experimental Oncology, KU Leuven, Leuven Cancer Institute, Leuven, Belgium
| | - Agnieszka Wozniak
- Department of Oncology, Laboratory of Experimental Oncology, KU Leuven, Leuven Cancer Institute, Leuven, Belgium
| | - Karo Wyns
- Department of Oncology, Laboratory of Experimental Oncology, KU Leuven, Leuven Cancer Institute, Leuven, Belgium
| | - Nanna Merikoski
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Sami Salmikangas
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jianmin Duan
- Duan Pharmaceutical Consulting Inc., Laval, Canada
| | | | | | - Tom Böhling
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Patrick Schöffski
- Department of Oncology, Laboratory of Experimental Oncology, KU Leuven, Leuven Cancer Institute, Leuven, Belgium
| | - Harri Sihto
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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Yang B, Wang M, Wu Z, Tan J, Meng Y, Zhang T, Zan L, Yang W. Perilipin1 mediates milk fat synthesis in bovine mammary epithelial cells through SREBP1 phosphorylation. Anim Biotechnol 2025; 36:2497915. [PMID: 40338730 DOI: 10.1080/10495398.2025.2497915] [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: 02/27/2025] [Accepted: 04/21/2025] [Indexed: 05/10/2025]
Abstract
This study investigates the role of Perilipin1 (PLIN1) in milk fat synthesis in bovine mammary epithelial cells (BMECs) and its regulatory mechanisms, aiming to provide a foundation for improving milk fat content through molecular breeding. BMECs were used as a model to analyze the effects of PLIN1 overexpression (OE-PLIN1) and interference (si-PLIN1) on milk fat synthesis and lipid-related gene expression using RT-qPCR, Western blot, and Oil Red O staining. Results show that OE-PLIN1 significantly enhances triglyceride (TAG) accumulation in BMECs (P < 0.01), upregulates lipid synthesis-related genes (such as PPARγ, C/EBPα, C/EBPβ, FABP4, FASN) (P < 0.05), and downregulates the mRNA expression of lipid breakdown-related genes (HSL, ATGL) (P < 0.05). Conversely, si-PLIN1 significantly reduces TAG accumulation (P < 0.05) and lowers the expression of lipid synthesis and breakdown genes (P < 0.05). Additionally, OE-PLIN1 combined with SREBP1 siRNA interference (si-SREBP1) did not have a significant impact on the mRNA and protein levels of SREBP1, but it significantly altered SREBP1's phosphorylation, indicating that SREBP1 interference inhibits PLIN1's effect on milk fat synthesis. This study suggests that PLIN1 promotes milk fat synthesis in BMECs via regulating SREBP1 activity, offering a new strategy for enhancing milk fat content in dairy cattle.
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Affiliation(s)
- Benshun Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Meng Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhangqing Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jianbing Tan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yanhong Meng
- Shaanxi Qinbao Animal Husbandry Co., LTD, Yangling, China
| | - Taoping Zhang
- Shaanxi Qinbao Animal Husbandry Co., LTD, Yangling, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wucai Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
- Northwest A&F University Shenzhen Research Institute, Shenzhen, China
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38
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Zhang Y, Mo C, Ai P, He X, Xiao Q, Yang X. Pharmacomicrobiomics: a new field contributing to optimizing drug therapy in Parkinson's disease. Gut Microbes 2025; 17:2454937. [PMID: 39875349 PMCID: PMC11776486 DOI: 10.1080/19490976.2025.2454937] [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] [Received: 06/17/2024] [Revised: 11/19/2024] [Accepted: 01/13/2025] [Indexed: 01/30/2025] Open
Abstract
Gut microbiota, which act as a determinant of pharmacokinetics, have long been overlooked. In recent years, a growing body of evidence indicates that the gut microbiota influence drug metabolism and efficacy. Conversely, drugs also exert a substantial influence on the function and composition of the gut microbiota. Pharmacomicrobiomics, an emerging field focusing on the interplay of drugs and gut microbiota, provides a potential foundation for making certain advances in personalized medicine. Understanding the communication between gut microbiota and antiparkinsonian drugs is critical for precise treatment of Parkinson's disease. Here, we provide a historical overview of the interplay between gut microbiota and antiparkinsonian drugs. Moreover, we discuss potential mechanistic insights into the complex associations between gut microbiota and drug metabolism. In addition, we also draw attention to microbiota-based biomarkers for predicting antiparkinsonian drug efficacy and examine current state-of-the-art knowledge of microbiota-based strategies to optimize drug therapy in Parkinson's disease.
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Affiliation(s)
- Yi Zhang
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chengjun Mo
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Penghui Ai
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoqin He
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qin Xiao
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaodong Yang
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Ren X, Zhao L, Hao Y, Huang X, Lv G, Zhou X. Copper-instigated modulatory cell mortality mechanisms and progress in kidney diseases. Ren Fail 2025; 47:2431142. [PMID: 39805816 PMCID: PMC11734396 DOI: 10.1080/0886022x.2024.2431142] [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: 02/28/2024] [Revised: 06/23/2024] [Accepted: 11/13/2024] [Indexed: 01/16/2025] Open
Abstract
Copper is a vital cofactor in various enzymes, plays a pivotal role in maintaining cell homeostasis. When copper metabolism is disordered and mitochondrial dysfunction is impaired, programmed cell death such as apoptosis, paraptosis, pyroptosis, ferroptosis, cuproptosis, autophagy and necroptosis can be induced. In this review, we focus on the metabolic mechanisms of copper. In addition, we discuss the mechanism by which copper induces various programmed cell deaths. Finally, this review examines copper's involvement in prevalent kidney diseases such as acute kidney injury and chronic kidney disease. The findings indicate that the use of copper chelators or plant extracts can mitigate kidney damage by reducing copper accumulation, offering novel insights into the pathogenesis and treatment strategies for kidney diseases.
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Affiliation(s)
- Xiya Ren
- The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Limei Zhao
- The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yajie Hao
- The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiu Huang
- The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Guangna Lv
- The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiaoshuang Zhou
- Department of Nephrology, Shanxi Provincial People’s Hospital, The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi, China
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Shao N, Cai K, Hong Y, Wu L, Luo Q. USP9X suppresses ferroptosis in diabetic kidney disease by deubiquitinating Nrf2 in vitro. Ren Fail 2025; 47:2458761. [PMID: 39967230 PMCID: PMC11841168 DOI: 10.1080/0886022x.2025.2458761] [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: 08/21/2024] [Revised: 12/22/2024] [Accepted: 01/21/2025] [Indexed: 02/20/2025] Open
Abstract
Nuclear factor erythroid 2-related factor 2 (Nrf2) regulates many critical genes associated with iron storage and transportation, the activity of which is influenced by E3 ligase-mediated ubiquitination. We wondered whether there is a deubiquitinase that mediates the deubiquitination of Nrf2 to stabilize Nrf2 expression and further prevent diabetic kidney disease (DKD). High glucose (HG) was applied to induce an in vitro model of DKD. The effects of HG on HK-2 cell viability, apoptosis, Fe2+ level, Nrf2, and ubiquitin-specific protease 9X (USP9X) were assessed by cell counting kit-8 (CCK-8) assay, flow cytometry, iron assay, and Western blot. The direct interaction between Nrf2 and USP9X was analyzed using co-immunoprecipitation and ubiquitination assay. After transfection and ferrostatin-1 (Fer-1) intervention, Nrf2 and USP9X levels, cell viability, apoptosis, and Fe2+ level were tested again. Reactive oxygen species (ROS), malondialdehyde (MDA), glutathione (GSH) contents, and ferroptosis-related markers were assessed by ROS assay kit, ELISA, and Western blot. HG reduced cell viability and levels of USP9X and Nrf2, while elevating apoptosis and Fe2+ level. An interaction between USP9X and Nrf2 has been verified and USP9X deubiquitinated Nrf2. Nrf2 up-regulation augmented the viability, GSH content, and ferroptosis-related protein expressions, while suppressing the apoptosis, Fe2+ level, MDA, and ROS content in HG-mediated HK-2 cells, which was reversed by USP9X silencing. Fer-1 offset the combined modulation of Nrf2 and siUSP9X on HG-induced HK-2 cells. USP9X mediates Nrf2 deubiquitinase to hamper the ferroptosis in DKD in vitro.
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Affiliation(s)
- Ningjun Shao
- Department of Nephrology, Ningbo No.2 Hospital, Ningbo, China
| | - Kedan Cai
- Department of Nephrology, Ningbo No.2 Hospital, Ningbo, China
| | - Yue Hong
- Department of Nephrology, Ningbo No.2 Hospital, Ningbo, China
| | - Lingping Wu
- Department of Nephrology, Ningbo No.2 Hospital, Ningbo, China
| | - Qun Luo
- Department of Nephrology, Ningbo No.2 Hospital, Ningbo, China
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Steinert RE, Rehman A, Sadabad MS, Milanese A, Wittwer-Schegg J, Burton JP, Spooren A. Microbial micronutrient sharing, gut redox balance and keystone taxa as a basis for a new perspective to solutions targeting health from the gut. Gut Microbes 2025; 17:2477816. [PMID: 40090884 PMCID: PMC11913388 DOI: 10.1080/19490976.2025.2477816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2024] [Revised: 02/05/2025] [Accepted: 03/05/2025] [Indexed: 03/18/2025] Open
Abstract
In health, the gut microbiome functions as a stable ecosystem maintaining overall balance and ensuring its own survival against environmental stressors through complex microbial interaction. This balance and protection from stressors is maintained through interactions both within the bacterial ecosystem as well as with its host. As a consequence, the gut microbiome plays a critical role in various physiological processes including maintaining the structure and function of the gut barrier, educating the gut immune system, and modulating the gut motor, digestive/absorptive, as well as neuroendocrine system all of which are crucial for human health and disease pathogenesis. Pre- and probiotics, widely available and clinically established, offer various health benefits primarily by beneficially modulating the gut microbiome. However, their clinical outcomes can vary significantly due to differences in host physiology, diets, individual microbiome compositions, and other environmental factors. This perspective paper highlights emerging scientific insights into the importance of microbial micronutrient sharing, gut redox balance, keystone species, and the gut barrier in maintaining a diverse and functional microbial ecosystem, and their relevance to human health. We propose a novel approach that targets microbial ecosystems and keystone taxa performance by supplying microbial micronutrients in the form of colon-delivered vitamins, and precision prebiotics [e.g. human milk oligosaccharides (HMOs) or synthetic glycans] as components of precisely tailored ingredient combinations to optimize human health. Such a strategy may effectively support and stabilize microbial ecosystems, providing a more robust and consistent approach across various individuals and environmental conditions, thus, overcoming the limitations of current single biotic solutions.
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Affiliation(s)
- Robert E. Steinert
- Health, Nutrition & Care (HNC), Dsm-Firmenich, Kaiseraugst, Switzerland
- Department of Surgery and Transplantation, University Hospital Zurich (USZ) and University of Zurich (UZH), Zürich, Switzerland
| | - Ateequr Rehman
- Health, Nutrition & Care (HNC), Dsm-Firmenich, Kaiseraugst, Switzerland
| | | | - Alessio Milanese
- Data Science, Science & Research, Dsm-Firmenich, Delft, Netherlands
| | | | - Jeremy P. Burton
- Department of Microbiology and Immunology, The University of Western Ontario, London, Canada
| | - Anneleen Spooren
- Health, Nutrition & Care (HNC), Dsm-Firmenich, Kaiseraugst, Switzerland
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42
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Chi J, Fan B, Li Y, Jiao Q, Li GY. Mitochondrial transplantation: a promising strategy for the treatment of retinal degenerative diseases. Neural Regen Res 2025; 20:3370-3387. [PMID: 39851134 PMCID: PMC11974652 DOI: 10.4103/nrr.nrr-d-24-00851] [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: 07/30/2024] [Revised: 09/11/2024] [Accepted: 10/24/2024] [Indexed: 01/26/2025] Open
Abstract
The retina, a crucial neural tissue, is responsible for transforming light signals into visual information, a process that necessitates a significant amount of energy. Mitochondria, the primary powerhouses of the cell, play an integral role in retinal physiology by fulfilling the high-energy requirements of photoreceptors and secondary neurons through oxidative phosphorylation. In a healthy state, mitochondria ensure proper visual function by facilitating efficient conversion and transduction of visual signals. However, in retinal degenerative diseases, mitochondrial dysfunction significantly contributes to disease progression, involving a decline in membrane potential, the occurrence of DNA mutations, increased oxidative stress, and imbalances in quality-control mechanisms. These abnormalities lead to an inadequate energy supply, the exacerbation of oxidative damage, and the activation of cell death pathways, ultimately resulting in neuronal injury and dysfunction in the retina. Mitochondrial transplantation has emerged as a promising strategy for addressing these challenges. This procedure aims to restore metabolic activity and function in compromised cells through the introduction of healthy mitochondria, thereby enhancing the cellular energy production capacity and offering new strategies for the treatment of retinal degenerative diseases. Although mitochondrial transplantation presents operational and safety challenges that require further investigation, it has demonstrated potential for reviving the vitality of retinal neurons. This review offers a comprehensive examination of the principles and techniques underlying mitochondrial transplantation and its prospects for application in retinal degenerative diseases, while also delving into the associated technical and safety challenges, thereby providing references and insights for future research and treatment.
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Affiliation(s)
- Jing Chi
- Department of Ophthalmology, The Second Norman Bethune Hospital of Jilin University, Changchun, Jilin Province, China
| | - Bin Fan
- Department of Ophthalmology, The Second Norman Bethune Hospital of Jilin University, Changchun, Jilin Province, China
| | - Yulin Li
- Department of Ophthalmology, The Second Norman Bethune Hospital of Jilin University, Changchun, Jilin Province, China
| | - Qing Jiao
- Department of Ophthalmology, The Second Norman Bethune Hospital of Jilin University, Changchun, Jilin Province, China
| | - Guang-Yu Li
- Department of Ophthalmology, The Second Norman Bethune Hospital of Jilin University, Changchun, Jilin Province, China
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He J, Li L, Hu H. Causal associations between circulating metabolites and chronic kidney disease: a Mendelian randomization study. Ren Fail 2025; 47:2498090. [PMID: 40302304 PMCID: PMC12044913 DOI: 10.1080/0886022x.2025.2498090] [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: 12/08/2024] [Revised: 03/30/2025] [Accepted: 04/13/2025] [Indexed: 05/02/2025] Open
Abstract
BACKGROUND Circulating metabolites have been associated with cross-sectional renal function in population-based research. Nevertheless, there is currently little proof to support the idea that metabolites either cause or prevent renal function. New treatment targets and ways to screen individuals with impaired renal function will be made possible via an in-depth analysis of the causal relationship between blood metabolites and renal function. METHODS We assessed the causal relationship between 452 serum metabolites and six renal phenotypes (CKD, rapid progression to CKD [CKDi25], rapid eGFR decline [CKD rapid3], dialysis, estimated glomerular filtration rate, and blood urea nitrogen) using univariate Mendelian randomization, primarily employing the inverse variance weighted method with robust sensitivity analyses. Heterogeneity and pleiotropy were examined via Cochrane's Q test and MR-Egger regression, and statistical significance was adjusted using Bonferroni correction. To assess potential adverse effects of metabolite modulation, we conducted a phenome-wide Mendelian randomization analysis, followed by multivariate Mendelian randomization to adjust for confounders. RESULTS We identified glycine and N-acetylornithine as potential causal mediators of CKD and renal dysfunction. Notably, lowering glycine levels may increase the risk of cholelithiasis and cholecystitis, while reducing N-acetylornithine could have unintended effects on tinnitus. CONCLUSION Glycine and N-acetylornithine represent promising therapeutic targets for CKD and renal function preservation, but their modulation requires careful risk-benefit assessment to avoid adverse effects.
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Affiliation(s)
- Jie He
- Department of Radiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
| | - Lin Li
- Department of Radiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
| | - Hongjie Hu
- Department of Radiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
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44
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Pancsa R, Andreev DE, Dean K. The implication of non-AUG-initiated N-terminally extended proteoforms in cancer. RNA Biol 2025; 22:1-18. [PMID: 40276932 PMCID: PMC12045569 DOI: 10.1080/15476286.2025.2498203] [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: 01/15/2025] [Revised: 04/03/2025] [Accepted: 04/21/2025] [Indexed: 04/26/2025] Open
Abstract
Dysregulated translation is a hallmark of cancer, and recent genome-wide studies in tumour cells have uncovered widespread translation of non-canonical reading frames that often initiate at non-AUG codons. If an upstream non-canonical start site is located within a frame with an annotated coding sequence (CDS), such translation events can lead to the production of proteoforms with altered N-termini (PANTs). Certain examples of PANTs from oncogenes (e.g. c-MYC) and tumour suppressors (e.g. PTEN) have been previously linked to cancer. We have performed a systematic computational analysis on recently identified non-AUG initiation-derived N-terminal extensions of cancer-associated proteins, and we discuss how these extended proteoforms may acquire new oncogenic properties. We identified a loss of stability for the N-terminally extended proteoforms of oncogenes TCF-4 and SOX2. Furthermore, we discovered likely functional short linear motifs within the N-terminal extensions of oncogenes and tumour suppressors (SOX2, SUFU, SFPQ, TOP1 and SPEN/SHARP) that could provide an explanation for previously described functionalities or interactions of the proteins. In all, we identify novel cases where PANTs likely show different localization, functions, partner binding or turnover rates compared to the annotated proteoforms. Therefore, we propose that alterations in the stringency of translation initiation, often seen under conditions of cellular stress, may result in reprogramming of translation to generate novel PANTs that influence cancer progression.
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Affiliation(s)
- Rita Pancsa
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Dmitry E. Andreev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Kellie Dean
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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Zhang X, Di Y, Zhang Y, Hu Y, Chi M, Kang J, Zheng Y, Wang H, Wang Y, Chen J, Zhang X. Hypermutability of Mycolicibacterium smegmatis due to ribonucleotide reductase-mediated oxidative homeostasis and imbalanced dNTP pools. Emerg Microbes Infect 2025; 14:2480698. [PMID: 40099407 PMCID: PMC11948356 DOI: 10.1080/22221751.2025.2480698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2024] [Revised: 02/09/2025] [Accepted: 03/12/2025] [Indexed: 03/19/2025]
Abstract
Ribonucleotide reductase (RNR) catalyzes the synthesis of four deoxyribonucleoside triphosphates (dNTPs), which are essential for DNA replication. Although dNTP imbalances reduce replication fidelity and elevate mutation rates, the impact of RNR dysfunction on Mycobacterium tuberculosis (Mtb) physiology and drug resistance remains unknown. Here, we constructed inducible knockdown strains for the RNR R1 subunit NrdE in Mtb and Mycolicibacterium smegmatis (Msm). NrdE knockdown significantly impaired growth and metabolic imbalances, indirectly disrupting oxidative homeostasis and mycolic acid synthesis, while increasing levels of intracellular ROS accumulation and enhancing cell wall permeability. Additionally, we developed genomic mutant strains, Msm-Y252A and Msm-Q255A, featuring targeted point mutations in the substrate-specific site (S-site) of the RNR loop domain, which determines NDP reduction specificity. The Msm-Y252A displayed a 1.9-fold decrease in dATP and increases in dGTP (1.6-fold), dTTP (9.0-fold), and dCTP (1.3-fold). In contrast, Msm-Q255A exhibited elevated intracellular levels of dGTP (1.6-fold), dTTP (6.1-fold), and dATP (1.5-fold), while dCTP levels remained unchanged. Neither the NrdE knockdown strain nor the S-site mutants exhibited direct resistance development; however, they both showed genomic instability, enhancing the emergence of rifampicin-resistant mutants, even with a 70-fold and a 25-fold increase in mutation frequency for Msm-Y252A and Msm-Q255A, respectively. This study demonstrates that NrdE is integral to Mycobacterium survival and genomic stability and that its RNR dysfunction creates a mutagenic environment under selective pressure, indirectly contributes to the development of drug resistance, positioning NrdE as an effective target for therapeutic strategies and a valuable molecular marker for early detection of drug-resistant Mtb.
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Affiliation(s)
- Xiao Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Yuchang Di
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Yu Zhang
- Shanghai Sci-Tech Inno Center for Infection & Immunity, Shanghai, People’s Republic of China
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
| | - Youwei Hu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Mingzhe Chi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Jian Kang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Yuqing Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Hengyu Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Yu Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Jiazhen Chen
- Shanghai Sci-Tech Inno Center for Infection & Immunity, Shanghai, People’s Republic of China
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
| | - Xuelian Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
- Shanghai Sci-Tech Inno Center for Infection & Immunity, Shanghai, People’s Republic of China
- MOE Engineering Research Center of Gene Technology and Shanghai Engineering Research Center of Industrial Microorganism, Fudan University, Shanghai, People's Republic of China
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Zhuang JL, Yu XH, Liu HG, Tang P, Deng HP, Li J, Zhou JQ, Zhang ZJ. Potential role of hemopexin in venous thromboembolism (VTE) mediated through effects on apoptosis-related proteins. Hematology 2025; 30:2475262. [PMID: 40067765 DOI: 10.1080/16078454.2025.2475262] [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: 09/01/2024] [Accepted: 02/28/2025] [Indexed: 04/07/2025] Open
Abstract
OBJECTIVE The limited understanding of venous thromboembolism (VTE) has hindered the development of novel treatment approaches. This study aimed to identify critical factors underlying VTE. METHODS The isobaric tags for relative and absolute quantitation (iTRAQ) method was applied to identify differentially expressed proteins in plasma samples from patients with VTE and healthy volunteers. Gene overexpression and knockdown techniques were used for cultured human umbilical vein endothelial cells (HUVECs) and VTE mouse models. Thrombosis and apoptosis related to the identified proteins were verified using qRT-PCR, western blot, and flow cytometry analyses. RESULTS iTRAQ analysis revealed significant upregulation of keratin 1, pro-platelet basic protein, and hemopexin (HPX) in the plasma of VTE patients. HPX was highly expressed in both plasma and GSE19151 and GSE48000 datasets. qRT-PCR and western blot results for HPX overexpressing HUVECs and VTE mouse models revealed that HPX positively regulated the expression of platelet endothelium aggregation receptor 1 and von Willebrand factor, but negatively regulated the expression of serpin family D member 1 and alpha-2-macroglobulin. Flow cytometry revealed that HPX exhibited pro-apoptotic activity in HPX overexpressing HUVECs. Furthermore, HPX elevated cleaved caspase-3 expression and inhibited B-cell lymphoma-2 expression in HUVECs and VTE mouse models. CONCLUSION HPX exhibits possible prothrombotic activity by regulating thrombosis - apoptosis-related proteins.
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Affiliation(s)
- Jun-Li Zhuang
- Department of Vascular Surgery, Renmin Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Xiao-Hui Yu
- Department of Vascular Surgery, Renmin Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Hua-Gang Liu
- Department of Vascular Surgery, Renmin Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Peng Tang
- Department of Vascular Surgery, Renmin Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Hong-Ping Deng
- Department of Vascular Surgery, Renmin Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Jie Li
- Department of Vascular Surgery, Renmin Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Jiang-Qiao Zhou
- Department of Organ Transplantation, Renmin Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Zhong-Jun Zhang
- Department of Vascular Surgery, Renmin Hospital of Xishui, Huanggang, People's Republic of China
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Yang X, Gao X, Jiang X, Yue K, Luo P. Targeting capabilities of engineered extracellular vesicles for the treatment of neurological diseases. Neural Regen Res 2025; 20:3076-3094. [PMID: 39435635 PMCID: PMC11881733 DOI: 10.4103/nrr.nrr-d-24-00462] [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: 04/23/2024] [Revised: 07/15/2024] [Accepted: 09/07/2024] [Indexed: 10/23/2024] Open
Abstract
Recent advances in research on extracellular vesicles have significantly enhanced their potential as therapeutic agents for neurological diseases. Owing to their therapeutic properties and ability to cross the blood-brain barrier, extracellular vesicles are recognized as promising drug delivery vehicles for various neurological conditions, including ischemic stroke, traumatic brain injury, neurodegenerative diseases, glioma, and psychosis. However, the clinical application of natural extracellular vesicles is hindered by their limited targeting ability and short clearance from the body. To address these limitations, multiple engineering strategies have been developed to enhance the targeting capabilities of extracellular vesicles, thereby enabling the delivery of therapeutic contents to specific tissues or cells. Therefore, this review aims to highlight the latest advancements in natural and targeting-engineered extracellular vesicles, exploring their applications in treating traumatic brain injury, ischemic stroke, Parkinson's disease, Alzheimer's disease, amyotrophic lateral sclerosis, glioma, and psychosis. Additionally, we summarized recent clinical trials involving extracellular vesicles and discussed the challenges and future prospects of using targeting-engineered extracellular vesicles for drug delivery in treating neurological diseases. This review offers new insights for developing highly targeted therapies in this field.
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Affiliation(s)
- Xinyu Yang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi Province, China
| | - Xiangyu Gao
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi Province, China
| | - Xiaofan Jiang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi Province, China
| | - Kangyi Yue
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi Province, China
| | - Peng Luo
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi Province, China
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48
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Aldali F, Deng C, Nie M, Chen H. Advances in therapies using mesenchymal stem cells and their exosomes for treatment of peripheral nerve injury: state of the art and future perspectives. Neural Regen Res 2025; 20:3151-3171. [PMID: 39435603 PMCID: PMC11881730 DOI: 10.4103/nrr.nrr-d-24-00235] [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: 02/26/2024] [Revised: 07/26/2024] [Accepted: 08/26/2024] [Indexed: 10/23/2024] Open
Abstract
"Peripheral nerve injury" refers to damage or trauma affecting nerves outside the brain and spinal cord. Peripheral nerve injury results in movements or sensation impairments, and represents a serious public health problem. Although severed peripheral nerves have been effectively joined and various therapies have been offered, recovery of sensory or motor functions remains limited, and efficacious therapies for complete repair of a nerve injury remain elusive. The emerging field of mesenchymal stem cells and their exosome-based therapies hold promise for enhancing nerve regeneration and function. Mesenchymal stem cells, as large living cells responsive to the environment, secrete various factors and exosomes. The latter are nano-sized extracellular vesicles containing bioactive molecules such as proteins, microRNA, and messenger RNA derived from parent mesenchymal stem cells. Exosomes have pivotal roles in cell-to-cell communication and nervous tissue function, offering solutions to changes associated with cell-based therapies. Despite ongoing investigations, mesenchymal stem cells and mesenchymal stem cell-derived exosome-based therapies are in the exploratory stage. A comprehensive review of the latest preclinical experiments and clinical trials is essential for deep understanding of therapeutic strategies and for facilitating clinical translation. This review initially explores current investigations of mesenchymal stem cells and mesenchymal stem cell-derived exosomes in peripheral nerve injury, exploring the underlying mechanisms. Subsequently, it provides an overview of the current status of mesenchymal stem cell and exosome-based therapies in clinical trials, followed by a comparative analysis of therapies utilizing mesenchymal stem cells and exosomes. Finally, the review addresses the limitations and challenges associated with use of mesenchymal stem cell-derived exosomes, offering potential solutions and guiding future directions.
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Affiliation(s)
- Fatima Aldali
- Department of Rehabilitation Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Chunchu Deng
- Department of Rehabilitation Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Mingbo Nie
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Hong Chen
- Department of Rehabilitation Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
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Wang Z, Wang S, Liu X, Shi H, Zhang W, Yang Z, Feng L, Ji A, Liang Z, Liu J, Zhang L, Zhang Y. Discovery of specific protein markers in multiple body fluids and their application in forensic science. Talanta 2025; 293:128032. [PMID: 40187281 DOI: 10.1016/j.talanta.2025.128032] [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: 01/10/2025] [Revised: 03/24/2025] [Accepted: 03/25/2025] [Indexed: 04/07/2025]
Abstract
Identification of multiple body fluids is crucial for the reconstruction and corroboration of crime event. However, for the body fluids with high component similarities, such as peripheral blood and menstrual blood, reliable distinguishing markers are still lacking. Furthermore, a comprehensive protein marker assay for multiple body fluids is urgently necessary for complex crime events. Herein, we established a highly specific and detectable method for discovering protein markers in peripheral blood, menstrual blood, saliva, semen and vaginal fluid through integrating in-depth discovery proteomics and a two-step targeted screening approach. Four menstrual blood markers with high endometrial specificities were identified for differentiation from peripheral blood and exhibited moderate protein concentrations for reproducible analysis with a protein quantitation CV value of 8.66%. Finally, a targeted discrimination method with 16 protein markers was established. We successfully identified 47 blind samples with 100% specificity and detection rate, sourced from five types of body fluids and presented on matrices such as cotton, tissues, slides or fluid. Overall, this work developed an effective method for discovering body fluid biomarkers, obtained specific protein markers to identify five kinds of body fluids and their targeted monitoring will show great significance for forensic science.
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Affiliation(s)
- Zhiting Wang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Songduo Wang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Xinxin Liu
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Huixia Shi
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Weijie Zhang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; DP Technology, Beijing, 100089, China
| | - Zhiyuan Yang
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Lei Feng
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Anquan Ji
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Zhen Liang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Jianhui Liu
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China.
| | - Lihua Zhang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Yukui Zhang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
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Tong Q, Shen W, Zhang L, Cao Y, Zou X, Shi T, Zhuang RX, Liu S, Xi J. A "turn-on" fluorescence polyethyleneimine-based nanosensor chemosensor for sensing of l-lysine. Talanta 2025; 293:128045. [PMID: 40184936 DOI: 10.1016/j.talanta.2025.128045] [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: 12/10/2024] [Revised: 03/26/2025] [Accepted: 03/28/2025] [Indexed: 04/07/2025]
Abstract
A novel polymeric nanosensor (named PEINAC) based on polyethyleneimine (PEI), was designed for the selective fluorescence detection of l-lysine (L-Lys) in aqueous solutions. The sensor was synthesized through a one-step, three-component reaction involving orthophthalaldehyde (OPA), PEI, and acetylcysteine. This reaction simultaneously facilitated the creation of an isoindole fluorophore, which was chemically attached to the PEI backbone. The structural properties, size, and morphology of PEINAC were thoroughly analyzed using various characterization techniques. When introduced into a buffered solution at pH 7.0, PEINAC demonstrated high specificity for L-Lys, inducing a marked fluorescence enhancement at 450 nm upon excitation at 367 nm. The fluorescence intensity exhibited a linear relationship with L-Lys concentration, ranging from 1 μM to 1000 μM, with a detection limit of 0.13 μM. Notably, the sensor exhibited excellent selectivity, showing no significant interference from other biomolecules and common transition metal ions and anions. This sensor was successfully applied for L-Lys quantification in blood and urine samples and for cellular L-Lys imaging, demonstrating its potential in various analytical and biomedical applications.
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Affiliation(s)
- Qiao Tong
- Hangzhou Xixi Hospital, Hangzhou, 310023, Zhejiang, China
| | - Weijie Shen
- Hangzhou Xixi Hospital, Hangzhou, 310023, Zhejiang, China
| | - Lu Zhang
- Hangzhou Xixi Hospital, Hangzhou, 310023, Zhejiang, China
| | - Yu Cao
- Hangzhou Xixi Hospital, Hangzhou, 310023, Zhejiang, China
| | - Xi Zou
- Hangzhou Xixi Hospital, Hangzhou, 310023, Zhejiang, China
| | - Tingting Shi
- Hangzhou Xixi Hospital, Hangzhou, 310023, Zhejiang, China
| | | | - Shourong Liu
- Hangzhou Xixi Hospital, Hangzhou, 310023, Zhejiang, China.
| | - Jianjun Xi
- Hangzhou Xixi Hospital, Hangzhou, 310023, Zhejiang, China.
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