1
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Kim HW, Lee JW, Yoon HS, Park HW, Lee YI, Lee SK, Whang J, Kim JS. Restriction of mitochondrial oxidation of glutamine or fatty acids enhances intracellular growth of Mycobacterium abscessus in macrophages. Virulence 2025; 16:2454323. [PMID: 39828906 PMCID: PMC11749347 DOI: 10.1080/21505594.2025.2454323] [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: 08/18/2024] [Revised: 11/28/2024] [Accepted: 01/12/2025] [Indexed: 01/22/2025] Open
Abstract
Mycobacterium abscessus (Mab), a nontuberculous mycobacterium, is increasing in prevalence worldwide and causes treatment-refractory pulmonary diseases. However, how Mab rewires macrophage energy metabolism to facilitate its survival is poorly understood. We compared the metabolic profiles of murine bone marrow-derived macrophages (BMDMs) infected with smooth (S)- and rough (R)-type Mab using extracellular flux technology. Mab infection shifted BMDMs towards a more energetic phenotype, marked by increased oxidative phosphorylation (OXPHOS) and glycolysis, with a significantly greater enhancement in OXPHOS. This metabolic adaptation was characterized by enhanced ATP production rates, particularly in cells infected with S-type Mab, highlighting OXPHOS as a key energy source. Notably, Mab infection also modulated mitochondrial substrate preferences, increasing fatty acid oxidation capabilities while revealing significant changes in glutamine dependency and flexibility. R-type Mab infections exhibited a marked decrease in glutamine reliance but enhanced metabolic flexibility and capacity. Furthermore, targeting metabolic pathways related to glutamine and fatty acid oxidation exacerbated Mab growth within macrophages, suggesting these pathways play a protective role against infection. These insights advance our understanding of Mab's impact on host cell metabolism and propose a novel avenue for therapeutic intervention. By manipulating host mitochondrial metabolism, we identify a potential host-directed therapeutic strategy against Mab, offering a promising alternative to conventional treatments beleaguered by drug resistance. This study underscores the importance of exploring metabolic interventions to combat Mab infection, paving the way for innovative approaches in the fight against this formidable pathogen.
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Affiliation(s)
- Ho Won Kim
- Myunggok Medical Research Institute, College of Medicine, Konyang University, Daejeon, South Korea
| | - Ji Won Lee
- Myunggok Medical Research Institute, College of Medicine, Konyang University, Daejeon, South Korea
| | - Hoe Sun Yoon
- Myunggok Medical Research Institute, College of Medicine, Konyang University, Daejeon, South Korea
| | - Hwan-Woo Park
- Department of Cell Biology, Konyang University Hospital and College of Medicine, Daejeon, South Korea
| | | | - Sung Ki Lee
- Department of Obstetrics and Gynecology, Konyang University Hospital, Daejeon, South Korea
| | - Jake Whang
- Korea Mycobacterium Resource Center (KMRC), Department of Research and Development, The Korean Institute of Tuberculosis, Osong, South Korea
| | - Jong-Seok Kim
- Myunggok Medical Research Institute, College of Medicine, Konyang University, Daejeon, South Korea
- Department of Cell Biology, Konyang University Hospital and College of Medicine, Daejeon, South Korea
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2
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Gao S, Zhu R, Qin Y, Tang W, Zhou H. Sg-snn: a self-organizing spiking neural network based on temporal information. Cogn Neurodyn 2025; 19:14. [PMID: 39801909 PMCID: PMC11718035 DOI: 10.1007/s11571-024-10199-6] [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: 07/28/2024] [Revised: 10/21/2024] [Accepted: 11/06/2024] [Indexed: 01/16/2025] Open
Abstract
Neurodynamic observations indicate that the cerebral cortex evolved by self-organizing into functional networks, These networks, or distributed clusters of regions, display various degrees of attention maps based on input. Traditionally, the study of network self-organization relies predominantly on static data, overlooking temporal information in dynamic neuromorphic data. This paper proposes Temporal Self-Organizing (TSO) method for neuromorphic data processing using a spiking neural network. The TSO method incorporates information from multiple time steps into the selection strategy of the Best Matching Unit (BMU) neurons. It enables the coupled BMUs to radiate the weight across the same layer of neurons, ultimately forming a hierarchical self-organizing topographic map of concern. Additionally, we simulate real neuronal dynamics, introduce a glial cell-mediated Glial-LIF (Leaky Integrate-and-fire) model, and adjust multiple levels of BMUs to optimize the attention topological map.Experiments demonstrate that the proposed Self-organizing Glial Spiking Neural Network (SG-SNN) can generate attention topographies for dynamic event data from coarse to fine. A heuristic method based on cognitive science effectively guides the network's distribution of excitatory regions. Furthermore, the SG-SNN shows improved accuracy on three standard neuromorphic datasets: DVS128-Gesture, CIFAR10-DVS, and N-Caltech 101, with accuracy improvements of 0.3%, 2.4%, and 0.54% respectively. Notably, the recognition accuracy on the DVS128-Gesture dataset reaches 99.3%, achieving state-of-the-art (SOTA) performance.
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Affiliation(s)
| | | | - Yu Qin
- Shanghai University, Shanghai, China
| | | | - Hao Zhou
- Shanghai University, Shanghai, China
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3
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Peng B, Yan MY, Chen YR, Sun F, Xiang XD, Liu D. The methyl-CpG binding domain 2 regulates peptidylarginine deiminase 4 expression and promotes neutrophil extracellular trap formation via the Janus kinase 2 signaling pathway in experimental severe asthma. Ann Med 2025; 57:2458207. [PMID: 39865866 PMCID: PMC11774153 DOI: 10.1080/07853890.2025.2458207] [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: 12/26/2024] [Accepted: 12/27/2024] [Indexed: 01/28/2025] Open
Abstract
OBJECTIVE The prognosis for severe asthma is poor, and the current treatment options are limited. The methyl-CpG binding domain protein 2 (MBD2) participates in neutrophil-mediated severe asthma through epigenetic regulation. Neutrophil extracellular traps (NETs) play a critical role in the pathogenesis of severe asthma. This study aims to detect if MBD2 can reduce NETs formation and the potential mechanism in severe asthma. METHODS A severe asthma model was established in C57BL/6 wild-type mice exposure to house dust mite (HDM), ovalbumin (OVA), and lipopolysaccharide (LPS). Enzyme-linked immunosorbent assay was used to measure the concentrations of IL-4, IL-17A, and IFN-γ in lung tissues. Flow cytometry was employed to determine the percentages of Th2, Th17, and Treg cells in lung tissues. Quantitative real-time polymerase chain reaction was utilized to assess the mRNA expression levels of MBD2, JAK2, and PAD4. Western blotting and immunofluorescence were conducted to detect the protein of MBD2, JAK2, PAD4, and CitH3. HL-60 cells were differentiated into neutrophil-like cells by culturing in a medium containing dimethyl sulfoxide and then stimulated with LPS. KCC-07, Ruxolitinib, and Cl-amidine were used to inhibit the expressions of MBD2, JAK2, and PAD4, respectively. RESULTS Severe asthma mice were characterized by pulmonary neutrophilic inflammation and increased formation of neutrophil extracellular traps (NETs). The expression of MBD2, JAK2, and PAD4 was elevated in severe asthma mice. Inhibiting the expression of MBD2, JAK2, and PAD4 reduced NETs formation and decreased airway inflammation scores, total cell counts and neutrophil counts in BALF, and percentage of Th2 and Th17 cell in lung tissues, whereas increasing Treg cell counts. In both severe asthma mice and HL-60-differentiated neutrophil-like cells in vitro, inhibiting MBD2 reduced the mRNA and protein expression of JAK2 and PAD4, and inhibiting JAK2 reduced the expression of PAD4 mRNA and protein. CONCLUSION MBD2 regulates PAD4 expression through the JAK2 signaling pathway to promote NETs formation in mice with severe asthma. Further bench-based and bedside-based studies targeting the MBD2, PAD4, and JAK2 signaling pathways will help open new avenues for drug development of severe asthma.
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Affiliation(s)
- Biao Peng
- Department of Pulmonary and Critical Care Medicine, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, Hunan, China
| | - Mu-Yun Yan
- Department of Pulmonary and Critical Care Medicine, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, Hunan, China
| | - Yun-Rong Chen
- Department of Pulmonary and Critical Care Medicine, Hunan Provincial People’s Hospital, (The First Affiliated Hospital of Hunan Normal University), Changsha, Hunan, China
| | - Fei Sun
- The Center for Biomedical Research, Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Xu-Dong Xiang
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Da Liu
- Department of Pulmonary and Critical Care Medicine, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, Hunan, China
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4
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Chen Y, Wei Y, Liu J, Zhu T, Zhou C, Zhang D. Spatial transcriptomics combined with single-nucleus RNA sequencing reveals glial cell heterogeneity in the human spinal cord. Neural Regen Res 2025; 20:3302-3316. [PMID: 38934400 DOI: 10.4103/nrr.nrr-d-23-01876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/30/2024] [Indexed: 06/28/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202511000-00032/figure1/v/2024-12-20T164640Z/r/image-tiff Glial cells play crucial roles in regulating physiological and pathological functions, including sensation, the response to infection and acute injury, and chronic neurodegenerative disorders. Glial cells include astrocytes, microglia, and oligodendrocytes in the central nervous system, and satellite glial cells and Schwann cells in the peripheral nervous system. Despite the greater understanding of glial cell types and functional heterogeneity achieved through single-cell and single-nucleus RNA sequencing in animal models, few studies have investigated the transcriptomic profiles of glial cells in the human spinal cord. Here, we used high-throughput single-nucleus RNA sequencing and spatial transcriptomics to map the cellular and molecular heterogeneity of astrocytes, microglia, and oligodendrocytes in the human spinal cord. To explore the conservation and divergence across species, we compared these findings with those from mice. In the human spinal cord, astrocytes, microglia, and oligodendrocytes were each divided into six distinct transcriptomic subclusters. In the mouse spinal cord, astrocytes, microglia, and oligodendrocytes were divided into five, four, and five distinct transcriptomic subclusters, respectively. The comparative results revealed substantial heterogeneity in all glial cell types between humans and mice. Additionally, we detected sex differences in gene expression in human spinal cord glial cells. Specifically, in all astrocyte subtypes, the levels of NEAT1 and CHI3L1 were higher in males than in females, whereas the levels of CST3 were lower in males than in females. In all microglial subtypes, all differentially expressed genes were located on the sex chromosomes. In addition to sex-specific gene differences, the levels of MT-ND4 , MT2A , MT-ATP6 , MT-CO3 , MT-ND2 , MT-ND3 , and MT-CO2 in all spinal cord oligodendrocyte subtypes were higher in females than in males. Collectively, the present dataset extensively characterizes glial cell heterogeneity and offers a valuable resource for exploring the cellular basis of spinal cord-related illnesses, including chronic pain, amyotrophic lateral sclerosis, and multiple sclerosis.
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Affiliation(s)
- Yali Chen
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Center of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Yiyong Wei
- Department of Anesthesiology, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, Guangdong Province, China
- Department of Anesthesiology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou Province, China
| | - Jin Liu
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Center of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Tao Zhu
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Cheng Zhou
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Center of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Donghang Zhang
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Center of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
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5
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Hashemolhosseini S, Gessler L. Crosstalk among canonical Wnt and Hippo pathway members in skeletal muscle and at the neuromuscular junction. Neural Regen Res 2025; 20:2464-2479. [PMID: 39248171 DOI: 10.4103/nrr.nrr-d-24-00417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 08/05/2024] [Indexed: 09/10/2024] Open
Abstract
Skeletal muscles are essential for locomotion, posture, and metabolic regulation. To understand physiological processes, exercise adaptation, and muscle-related disorders, it is critical to understand the molecular pathways that underlie skeletal muscle function. The process of muscle contraction, orchestrated by a complex interplay of molecular events, is at the core of skeletal muscle function. Muscle contraction is initiated by an action potential and neuromuscular transmission requiring a neuromuscular junction. Within muscle fibers, calcium ions play a critical role in mediating the interaction between actin and myosin filaments that generate force. Regulation of calcium release from the sarcoplasmic reticulum plays a key role in excitation-contraction coupling. The development and growth of skeletal muscle are regulated by a network of molecular pathways collectively known as myogenesis. Myogenic regulators coordinate the differentiation of myoblasts into mature muscle fibers. Signaling pathways regulate muscle protein synthesis and hypertrophy in response to mechanical stimuli and nutrient availability. Several muscle-related diseases, including congenital myasthenic disorders, sarcopenia, muscular dystrophies, and metabolic myopathies, are underpinned by dysregulated molecular pathways in skeletal muscle. Therapeutic interventions aimed at preserving muscle mass and function, enhancing regeneration, and improving metabolic health hold promise by targeting specific molecular pathways. Other molecular signaling pathways in skeletal muscle include the canonical Wnt signaling pathway, a critical regulator of myogenesis, muscle regeneration, and metabolic function, and the Hippo signaling pathway. In recent years, more details have been uncovered about the role of these two pathways during myogenesis and in developing and adult skeletal muscle fibers, and at the neuromuscular junction. In fact, research in the last few years now suggests that these two signaling pathways are interconnected and that they jointly control physiological and pathophysiological processes in muscle fibers. In this review, we will summarize and discuss the data on these two pathways, focusing on their concerted action next to their contribution to skeletal muscle biology. However, an in-depth discussion of the non-canonical Wnt pathway, the fibro/adipogenic precursors, or the mechanosensory aspects of these pathways is not the focus of this review.
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Affiliation(s)
- Said Hashemolhosseini
- Institute of Biochemistry, Medical Faculty, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany
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6
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Ma Y, Dong T, Luan F, Yang J, Miao F, Wei P. Interaction of major facilitator superfamily domain containing 2A with the blood-brain barrier. Neural Regen Res 2025; 20:2133-2152. [PMID: 39248155 PMCID: PMC11759009 DOI: 10.4103/nrr.nrr-d-24-00191] [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: 02/15/2024] [Revised: 06/02/2024] [Accepted: 07/08/2024] [Indexed: 09/10/2024] Open
Abstract
The functional and structural integrity of the blood-brain barrier is crucial in maintaining homeostasis in the brain microenvironment; however, the molecular mechanisms underlying the formation and function of the blood-brain barrier remain poorly understood. The major facilitator superfamily domain containing 2A has been identified as a key regulator of blood-brain barrier function. It plays a critical role in promoting and maintaining the formation and functional stability of the blood-brain barrier, in addition to the transport of lipids, such as docosahexaenoic acid, across the blood-brain barrier. Furthermore, an increasing number of studies have suggested that major facilitator superfamily domain containing 2A is involved in the molecular mechanisms of blood-brain barrier dysfunction in a variety of neurological diseases; however, little is known regarding the mechanisms by which major facilitator superfamily domain containing 2A affects the blood-brain barrier. This paper provides a comprehensive and systematic review of the close relationship between major facilitator superfamily domain containing 2A proteins and the blood-brain barrier, including their basic structures and functions, cross-linking between major facilitator superfamily domain containing 2A and the blood-brain barrier, and the in-depth studies on lipid transport and the regulation of blood-brain barrier permeability. This comprehensive systematic review contributes to an in-depth understanding of the important role of major facilitator superfamily domain containing 2A proteins in maintaining the structure and function of the blood-brain barrier and the research progress to date. This will not only help to elucidate the pathogenesis of neurological diseases, improve the accuracy of laboratory diagnosis, and optimize clinical treatment strategies, but it may also play an important role in prognostic monitoring. In addition, the effects of major facilitator superfamily domain containing 2A on blood-brain barrier leakage in various diseases and the research progress on cross-blood-brain barrier drug delivery are summarized. This review may contribute to the development of new approaches for the treatment of neurological diseases.
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Affiliation(s)
- Yilun Ma
- College of Pharmacy and First Clinical Medical College, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi Province, China
| | - Taiwei Dong
- College of Pharmacy and First Clinical Medical College, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi Province, China
| | - Fei Luan
- College of Pharmacy and First Clinical Medical College, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi Province, China
| | - Juanjuan Yang
- National Drug Clinical Trial Agency, The Second Affiliated Hospital of Shaanxi University of Chinese Medicine/Xixian New District Central Hospital, Xi′an, Shaanxi Province, China
| | - Feng Miao
- College of Pharmacy and First Clinical Medical College, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi Province, China
| | - Peifeng Wei
- National Drug Clinical Trial Agency, The Second Affiliated Hospital of Shaanxi University of Chinese Medicine/Xixian New District Central Hospital, Xi′an, Shaanxi Province, China
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7
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Prudinnik DS, Kussanova A, Vorobjev IA, Tikhonov A, Ataullakhanov FI, Barteneva NS. Deformability of Heterogeneous Red Blood Cells in Aging and Related Pathologies. Aging Dis 2025:AD.2024.0526. [PMID: 39012672 DOI: 10.14336/ad.2024.0526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 06/19/2024] [Indexed: 07/17/2024] Open
Abstract
Aging is interrelated with changes in red blood cell parameters and functionality. In this article, we focus on red blood cells (RBCs) and provide a review of the known changes associated with the characterization of RBC deformability in aging and related pathologies. The biophysical parameters complement the commonly used biochemical parameters and may contribute to a better understanding of the aging process. The power of the deformability measurement approach is well established in clinical settings. Measuring RBCs' deformability has the advantage of relative simplicity, and it reflects the complex effects developing in erythrocytes during aging. However, aging and related pathological conditions also promote heterogeneity of RBC features and have a certain impact on the variance in erythrocyte cell properties. The possible applications of deformability as an early biophysical biomarker of pathological states are discussed, and modulating PIEZO1 as a therapeutic target is suggested. The changes in RBCs' shape can serve as a proxy for deformability evaluation, leveraging single-cell analysis with imaging flow cytometry and artificial intelligence algorithms. The characterization of biophysical parameters of RBCs is in progress in humans and will provide a better understanding of the complex dynamics of aging.
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Affiliation(s)
- Dmitry S Prudinnik
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana 010000, Kazakhstan
| | - Aigul Kussanova
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana 010000, Kazakhstan
| | - Ivan A Vorobjev
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana 010000, Kazakhstan
| | - Alexander Tikhonov
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana 010000, Kazakhstan
| | - Fazly I Ataullakhanov
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Natasha S Barteneva
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana 010000, Kazakhstan
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8
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Wang Y, Zhou S, Wang X, Lu D, Yang J, Lu Y, Fan X, Li C, Wang Y. Electroactive membranes enhance in-situ alveolar ridge preservation via spatiotemporal electrical modulation of cell motility. Biomaterials 2025; 317:123077. [PMID: 39756273 DOI: 10.1016/j.biomaterials.2024.123077] [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: 08/22/2024] [Revised: 11/27/2024] [Accepted: 12/30/2024] [Indexed: 01/07/2025]
Abstract
Post-extraction alveolar bone resorption invariably compromises implant placement and aesthetic restoration outcomes. Current non-resorbable membranes exhibit limited efficacy in alveolar ridge preservation (ARP) due to insufficient cell recruitment and osteoinductive capabilities. Herein, we introduce a multifunctional electroactive membrane (PPy-BTO/P(VDF-TrFE), PB/PT) designed to spatiotemporally regulate cell migration and osteogenesis, harmonizing with the socket healing process. Initially, the membrane's endogenous-level surface potential recruits stem cells from the socket. Subsequently, adherent cell-migration-triggered forces generate on-demand piezopotential, stimulating intracellular calcium ion fluctuations and activating the Ca2+/calcineurin/NFAT1 signaling pathway via Cav3.2 channels. This enhances cell motility and osteogenic differentiation predominantly in the coronal socket region, counteracting the natural healing trajectory. The membrane's self-powered energy supply, proportional to cell migration velocity and manifested as nanoparticle deformation, mitigates ridge shrinkage, both independently and in conjunction with bone grafts. This energy-autonomous membrane, based on the spatiotemporal modulation of cell motility, presents a novel approach for in-situ ARP treatment and the development of 4D bionic scaffolds.
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Affiliation(s)
- Yanlan Wang
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Shiqi Zhou
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Xiaoshuang Wang
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Dongheng Lu
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Jinghong Yang
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Yu Lu
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Xiaolei Fan
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Changhao Li
- State Key Laboratory of Digital Medical Engineering, Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Sanya, 572025, China.
| | - Yan Wang
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China.
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9
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Saad H, El Baba B, Tfaily A, Kobeissy F, Gonzalez JG, Refai D, Rodts GR, Mustroph C, Gimbel D, Grossberg J, Barrow DL, Gary MF, Alawieh AM. Complement-dependent neuroinflammation in spinal cord injury: from pathology to therapeutic implications. Neural Regen Res 2025; 20:1324-1335. [PMID: 38845224 PMCID: PMC11624873 DOI: 10.4103/nrr.nrr-d-24-00116] [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: 01/28/2024] [Revised: 04/07/2024] [Accepted: 04/29/2024] [Indexed: 07/31/2024] Open
Abstract
Spinal cord injury remains a major cause of disability in young adults, and beyond acute decompression and rehabilitation, there are no pharmacological treatments to limit the progression of injury and optimize recovery in this population. Following the thorough investigation of the complement system in triggering and propagating cerebral neuroinflammation, a similar role for complement in spinal neuroinflammation is a focus of ongoing research. In this work, we survey the current literature investigating the role of complement in spinal cord injury including the sources of complement proteins, triggers of complement activation, and role of effector functions in the pathology. We study relevant data demonstrating the different triggers of complement activation after spinal cord injury including direct binding to cellular debris, and or activation via antibody binding to damage-associated molecular patterns. Several effector functions of complement have been implicated in spinal cord injury, and we critically evaluate recent studies on the dual role of complement anaphylatoxins in spinal cord injury while emphasizing the lack of pathophysiological understanding of the role of opsonins in spinal cord injury. Following this pathophysiological review, we systematically review the different translational approaches used in preclinical models of spinal cord injury and discuss the challenges for future translation into human subjects. This review emphasizes the need for future studies to dissect the roles of different complement pathways in the pathology of spinal cord injury, to evaluate the phases of involvement of opsonins and anaphylatoxins, and to study the role of complement in white matter degeneration and regeneration using translational strategies to supplement genetic models.
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Affiliation(s)
- Hassan Saad
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA, USA
| | - Bachar El Baba
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA, USA
| | - Ali Tfaily
- Department of Neurology, Yale University, New Haven, CT, USA
| | - Firas Kobeissy
- Center for Neurotrauma, Multiomics & Biomarkers (CNMB), Morehouse School of Medicine, Atlanta, GA, USA
| | | | - Daniel Refai
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA, USA
| | - Gerald R. Rodts
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA, USA
| | - Christian Mustroph
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA, USA
| | - David Gimbel
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA, USA
| | - Jonathan Grossberg
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA, USA
| | - Daniel L. Barrow
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA, USA
| | - Matthew F. Gary
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA, USA
| | - Ali M. Alawieh
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA, USA
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10
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Li M, Deng T, Chen Q, Jiang S, Li H, Li J, You S, Xie HQ, Shen B. A versatile platform based on matrix metalloproteinase-sensitive peptides for novel diagnostic and therapeutic strategies in arthritis. Bioact Mater 2025; 47:100-120. [PMID: 39897588 PMCID: PMC11787566 DOI: 10.1016/j.bioactmat.2025.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Revised: 01/11/2025] [Accepted: 01/12/2025] [Indexed: 02/04/2025] Open
Abstract
Matrix metalloproteinases (MMPs), coupled with other proteinases and glycanases, can degrade proteoglycans, collagens, and other extracellular matrix (ECM) components in inflammatory and non-inflammatory arthritis, making them important pathogenic molecules and ideal disease indicators and pharmaceutical intervention triggers. For MMP responsiveness, MMP-sensitive peptides (MSPs) are among the most easily synthesized and cost-effective substrates, with free terminal amine and/or carboxyl groups extensively employed in multiple designs. We hereby provide a comprehensive review over the mechanisms and advances in MSP applications for the management of arthritis. These applications include early and precise diagnosis of MMP activity via fluorescence probe technologies; acting as nanodrug carriers to enable on-demand drug release triggered by pathological microenvironments; and facilitating cartilage engineering through MMP-mediated degradation, which promotes cell migration, matrix synthesis, and tissue integration. Specifically, the ultra-sensitive MSP diagnostic probes could significantly advance the early diagnosis and detection of osteoarthritis (OA), while MSP-based drug carriers for rheumatoid arthritis (RA) can intelligently release anti-inflammatory drugs effectively during flare-ups, or even before symptoms manifest. The continuous progress in MSP development may acceleratedly lead to novel management regimens for arthropathy in the future.
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Affiliation(s)
- Mingyang Li
- Department of Orthopedics, Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Tao Deng
- Department of Orthopedics, Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Quan Chen
- Department of Orthopedics, Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Shenghu Jiang
- Department of Orthopedics, Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Hang Li
- Department of Orthopedics, Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Jiayi Li
- Department of Nephrology, The People's Hospital of Yubei District of Chongqing, Chongqing, China
| | - Shenglan You
- Animal Imaging Core Facilities, West China Hospital, Sichuan University, China
| | - Hui-qi Xie
- Department of Orthopedics, Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
- Stem Cell and Tissue Engineering Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Bin Shen
- Department of Orthopedics, Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
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11
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Liu Z, Pan C, Huang H. The role of axon guidance molecules in the pathogenesis of epilepsy. Neural Regen Res 2025; 20:1244-1257. [PMID: 39075893 PMCID: PMC11624883 DOI: 10.4103/nrr.nrr-d-23-01620] [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: 09/27/2023] [Revised: 12/06/2023] [Accepted: 02/21/2024] [Indexed: 07/31/2024] Open
Abstract
Current treatments for epilepsy can only manage the symptoms of the condition but cannot alter the initial onset or halt the progression of the disease. Consequently, it is crucial to identify drugs that can target novel cellular and molecular mechanisms and mechanisms of action. Increasing evidence suggests that axon guidance molecules play a role in the structural and functional modifications of neural networks and that the dysregulation of these molecules is associated with epilepsy susceptibility. In this review, we discuss the essential role of axon guidance molecules in neuronal activity in patients with epilepsy as well as the impact of these molecules on synaptic plasticity and brain tissue remodeling. Furthermore, we examine the relationship between axon guidance molecules and neuroinflammation, as well as the structural changes in specific brain regions that contribute to the development of epilepsy. Ample evidence indicates that axon guidance molecules, including semaphorins and ephrins, play a fundamental role in guiding axon growth and the establishment of synaptic connections. Deviations in their expression or function can disrupt neuronal connections, ultimately leading to epileptic seizures. The remodeling of neural networks is a significant characteristic of epilepsy, with axon guidance molecules playing a role in the dynamic reorganization of neural circuits. This, in turn, affects synapse formation and elimination. Dysregulation of these molecules can upset the delicate balance between excitation and inhibition within a neural network, thereby increasing the risk of overexcitation and the development of epilepsy. Inflammatory signals can regulate the expression and function of axon guidance molecules, thus influencing axonal growth, axon orientation, and synaptic plasticity. The dysregulation of neuroinflammation can intensify neuronal dysfunction and contribute to the occurrence of epilepsy. This review delves into the mechanisms associated with the pathogenicity of axon guidance molecules in epilepsy, offering a valuable reference for the exploration of therapeutic targets and presenting a fresh perspective on treatment strategies for this condition.
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Affiliation(s)
- Zheng Liu
- Department of Neurology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou Province, China
| | - Chunhua Pan
- Department of Neurology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou Province, China
| | - Hao Huang
- Department of Neurology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou Province, China
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12
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Fu H, Cheng J, Hu L, Heng BC, Zhang X, Deng X, Liu Y. Mitochondria-targeting materials and therapies for regenerative engineering. Biomaterials 2025; 316:123023. [PMID: 39708774 DOI: 10.1016/j.biomaterials.2024.123023] [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: 09/09/2024] [Revised: 12/03/2024] [Accepted: 12/13/2024] [Indexed: 12/23/2024]
Abstract
The hemostatic, inflammatory, proliferative, and remodeling phases of healing require precise spatiotemporal coordination and orchestration of numerous biological processes. As the primary energy generators in the cell, mitochondria play multifunctional roles in regulating metabolism, stress reactions, immunity, and cell density during the process of tissue regeneration. Mitochondrial dynamics involves numerous crucial processes, fusion, fission, autophagy, and translocation, which are all necessary for preserving mitochondrial function, distributing energy throughout cells, and facilitating cellular signaling. Tissue regeneration is specifically associated with mitochondrial dynamics due to perturbations of Ca2+, H2O2 and ROS levels, which can result in mitochondrial malfunction. Increasing evidence from multiple models suggests that clinical interventions or medicinal drugs targeting mitochondrial dynamics could be a promising approach. This review highlights significant advances in the understanding of mitochondrial dynamics in tissue regeneration, with specific attention on mitochondria-targeting biomaterials that accelerate multiple tissues' regeneration by regulating mitochondrial metabolism. The innovations in nanomaterials and nanosystems enhance mitochondrial-targeting therapies are critically examined with the prospects of modulating mitochondrial dynamics for new therapies in regenerative engineering.
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Affiliation(s)
- Hongying Fu
- Department of Dental Materials & Dental Medical Devices Testing Center & NMPA Key Laboratory for Dental Materials & Beijing Key Laboratory of Digital Stomatology, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices & National Center for Stomatology & National Clinical Research Center for Oral Diseases & NHC Research Center of Engineering and Technology for Computerized Dentistry, Peking University School and Hospital of Stomatology, Beijing, 100081, China; Institute of Advanced Clinical Medicine, Peking University, Beijing, 100191, China
| | - Jingrong Cheng
- Department of Dental Materials & Dental Medical Devices Testing Center & NMPA Key Laboratory for Dental Materials & Beijing Key Laboratory of Digital Stomatology, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices & National Center for Stomatology & National Clinical Research Center for Oral Diseases & NHC Research Center of Engineering and Technology for Computerized Dentistry, Peking University School and Hospital of Stomatology, Beijing, 100081, China; Institute of Advanced Clinical Medicine, Peking University, Beijing, 100191, China
| | - Le Hu
- Department of Dental Materials & Dental Medical Devices Testing Center & NMPA Key Laboratory for Dental Materials & Beijing Key Laboratory of Digital Stomatology, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices & National Center for Stomatology & National Clinical Research Center for Oral Diseases & NHC Research Center of Engineering and Technology for Computerized Dentistry, Peking University School and Hospital of Stomatology, Beijing, 100081, China; Institute of Advanced Clinical Medicine, Peking University, Beijing, 100191, China
| | - Boon Chin Heng
- Department of Dental Materials & Dental Medical Devices Testing Center & NMPA Key Laboratory for Dental Materials & Beijing Key Laboratory of Digital Stomatology, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices & National Center for Stomatology & National Clinical Research Center for Oral Diseases & NHC Research Center of Engineering and Technology for Computerized Dentistry, Peking University School and Hospital of Stomatology, Beijing, 100081, China; Institute of Advanced Clinical Medicine, Peking University, Beijing, 100191, China
| | - Xuehui Zhang
- Department of Dental Materials & Dental Medical Devices Testing Center & NMPA Key Laboratory for Dental Materials & Beijing Key Laboratory of Digital Stomatology, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices & National Center for Stomatology & National Clinical Research Center for Oral Diseases & NHC Research Center of Engineering and Technology for Computerized Dentistry, Peking University School and Hospital of Stomatology, Beijing, 100081, China; Institute of Advanced Clinical Medicine, Peking University, Beijing, 100191, China.
| | - Xuliang Deng
- Department of Dental Materials & Dental Medical Devices Testing Center & NMPA Key Laboratory for Dental Materials & Beijing Key Laboratory of Digital Stomatology, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices & National Center for Stomatology & National Clinical Research Center for Oral Diseases & NHC Research Center of Engineering and Technology for Computerized Dentistry, Peking University School and Hospital of Stomatology, Beijing, 100081, China; Department of Geriatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, 100081, China; Institute of Advanced Clinical Medicine, Peking University, Beijing, 100191, China.
| | - Yang Liu
- Department of Dental Materials & Dental Medical Devices Testing Center & NMPA Key Laboratory for Dental Materials & Beijing Key Laboratory of Digital Stomatology, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices & National Center for Stomatology & National Clinical Research Center for Oral Diseases & NHC Research Center of Engineering and Technology for Computerized Dentistry, Peking University School and Hospital of Stomatology, Beijing, 100081, China; Institute of Advanced Clinical Medicine, Peking University, Beijing, 100191, China.
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13
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Han R, Luo L, Wei C, Qiao Y, Xie J, Pan X, Xing J. Stiffness-tunable biomaterials provide a good extracellular matrix environment for axon growth and regeneration. Neural Regen Res 2025; 20:1364-1376. [PMID: 39075897 PMCID: PMC11624885 DOI: 10.4103/nrr.nrr-d-23-01874] [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: 11/14/2023] [Revised: 01/31/2024] [Accepted: 03/16/2024] [Indexed: 07/31/2024] Open
Abstract
Neuronal growth, extension, branching, and formation of neural networks are markedly influenced by the extracellular matrix-a complex network composed of proteins and carbohydrates secreted by cells. In addition to providing physical support for cells, the extracellular matrix also conveys critical mechanical stiffness cues. During the development of the nervous system, extracellular matrix stiffness plays a central role in guiding neuronal growth, particularly in the context of axonal extension, which is crucial for the formation of neural networks. In neural tissue engineering, manipulation of biomaterial stiffness is a promising strategy to provide a permissive environment for the repair and regeneration of injured nervous tissue. Recent research has fine-tuned synthetic biomaterials to fabricate scaffolds that closely replicate the stiffness profiles observed in the nervous system. In this review, we highlight the molecular mechanisms by which extracellular matrix stiffness regulates axonal growth and regeneration. We highlight the progress made in the development of stiffness-tunable biomaterials to emulate in vivo extracellular matrix environments, with an emphasis on their application in neural repair and regeneration, along with a discussion of the current limitations and future prospects. The exploration and optimization of the stiffness-tunable biomaterials has the potential to markedly advance the development of neural tissue engineering.
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Affiliation(s)
- Ronglin Han
- Department of Pathophysiology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan Province, China
| | - Lanxin Luo
- Department of Pathophysiology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan Province, China
| | - Caiyan Wei
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan Province, China
| | - Yaru Qiao
- Department of Pathophysiology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan Province, China
| | - Jiming Xie
- Department of Pathophysiology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan Province, China
| | - Xianchao Pan
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan Province, China
| | - Juan Xing
- Department of Pathophysiology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan Province, China
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14
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Hung GY, Wang CY, Feng KC, Tu CS, Cheng IC, Mana-Ay H, Hsiao HY, Lai PL, Chen PY. Manipulating Mg/Ca ratios in MgO-CaO-SiO 2 bioactive glass for achieving accelerated osteogenic differentiation of human adipose-derived stem cells. BIOMATERIALS ADVANCES 2025; 169:214189. [PMID: 39826260 DOI: 10.1016/j.bioadv.2025.214189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2024] [Revised: 12/30/2024] [Accepted: 01/14/2025] [Indexed: 01/22/2025]
Abstract
Cell-containing biomaterial is a promising material for treating nonunion or critical bone defect. Human adipose-derived stem cells (hADSCs) are suitable for bone repair due to their abundance in the abdomen, thighs, and buttocks. However, the low osteogenic capacities of hADSCs hinder their extended development for bone regeneration application. The present goal explores a novel MgO-CaO-SiO2 bioactive glass with suitable Mg/Ca ratios to enhance the osteogenic differentiation and bioactivity of hADSCs. The synthetic bioglass can be expressed as xMgO-(2-x)CaO-SiO2 (abbreviated as Mg(x)Ca(2-x)Si2, x = 0, 0.25, 0.5, 0.75, and 1). The expression levels of osteoblast-related genes (i.e., BMP2, RUNX2, DLX5, COL1A1, BGLAP2, and SPP1) were evaluated by reverse transcription-quantitative PCR (RT-PCR). The proteins involved in the p38/Akt/ERK signaling pathways were analyzed with Western blots. The results indicated that the extractions from the Mg(x)Ca(2-x)Si2 bioglass promoted hADSCs proliferation. Among the Mg(x)Ca(2-x)Si2 bioglass with different Mg/Ca ratios, the bioglass with a low Mg/Ca ratio (x = 0.25) presented greater osteogenic differentiation of hADSCs by promoting the p38 signaling pathway. Interestingly, the bioglass with low Mg/Ca ratio (x = 0.25) further presented on osteogenic potential with greater osteointegration in rat femoral defect model. This work provides the optimal Mg/Ca ratio in Mg(x)Ca(2-x)Si2 bioglass to promote the osteogenic induction of hADSCs and bone regeneration.
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Affiliation(s)
- Guan-Yi Hung
- International Ph.D. Program in Innovative Technology of Biomedical Engineering and Medical Devices, Ming Chi University of Technology, New Taipei City 24301, Taiwan
| | - Chi-Yun Wang
- International Ph.D. Program in Innovative Technology of Biomedical Engineering and Medical Devices, Ming Chi University of Technology, New Taipei City 24301, Taiwan
| | - Kuei-Chih Feng
- International Ph.D. Program in Innovative Technology of Biomedical Engineering and Medical Devices, Ming Chi University of Technology, New Taipei City 24301, Taiwan; Department of Mechanical Engineering, Ming Chi University of Technology, New Taipei City 24301, Taiwan
| | - Chi-Shun Tu
- International Ph.D. Program in Innovative Technology of Biomedical Engineering and Medical Devices, Ming Chi University of Technology, New Taipei City 24301, Taiwan; Department of Physics, Fu Jen Catholic University, New Taipei City 24205, Taiwan
| | - I-Chien Cheng
- International Ph.D. Program in Innovative Technology of Biomedical Engineering and Medical Devices, Ming Chi University of Technology, New Taipei City 24301, Taiwan
| | - Haidee Mana-Ay
- International Ph.D. Program in Innovative Technology of Biomedical Engineering and Medical Devices, Ming Chi University of Technology, New Taipei City 24301, Taiwan; Department of Physics, Silliman University, Dumaguete City 6200, Philippines
| | - Hui-Yi Hsiao
- International Ph.D. Program in Innovative Technology of Biomedical Engineering and Medical Devices, Ming Chi University of Technology, New Taipei City 24301, Taiwan; Department of Biomedical Sciences, Chang Gung University, Taoyuan City 33305, Taiwan; Center for Tissue Engineering, Chang Gung Memorial Hospital, Linkou, Taoyuan 33305, Taiwan.
| | - Po-Liang Lai
- International Ph.D. Program in Innovative Technology of Biomedical Engineering and Medical Devices, Ming Chi University of Technology, New Taipei City 24301, Taiwan; Bone and Joint Research Center, Department of Orthopedic Surgery, Chang Gung Memorial Hospital, Taoyuan City 33305, Taiwan; College of Medicine, Chang Gung University, Taoyuan City 33305, Taiwan.
| | - Pin-Yi Chen
- International Ph.D. Program in Innovative Technology of Biomedical Engineering and Medical Devices, Ming Chi University of Technology, New Taipei City 24301, Taiwan; Department of Mechanical Engineering, Chang Gung University, Taoyuan City 33302, Taiwan; Research Center for Intelligent Medical Devices, Ming Chi University of Technology, New Taipei City 24301, Taiwan.
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15
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Chen Y, Chen L, Wu J, Xu X, Yang C, Zhang Y, Chen X, Lin K, Zhang S. Throw out an oligopeptide to catch a protein: Deep learning and natural language processing-screened tripeptide PSP promotes Osteolectin-mediated vascularized bone regeneration. Bioact Mater 2025; 46:37-54. [PMID: 39734571 PMCID: PMC11681832 DOI: 10.1016/j.bioactmat.2024.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 09/26/2024] [Accepted: 11/06/2024] [Indexed: 12/31/2024] Open
Abstract
Angiogenesis is imperative for bone regeneration, yet the conventional cytokine therapies have been constrained by prohibitive costs and safety apprehensions. It is urgent to develop a safer and more efficient therapeutic alternative. Herein, utilizing the methodologies of Deep Learning (DL) and Natural Language Processing (NLP), we proposed a paradigm algorithm that amalgamates Word2vec with a TF-IDF variant, TF-IIDF, to deftly discern potential pro-angiogenic peptides from intrinsically disordered regions (IDRs) of 262 related proteins, where are fertile grounds for developing safer and highly promising bioactive peptides. After the evaluation of the candidate oligopeptides, one tripeptide, PSP, emerged as particularly notable for its exceptional ability to stimulate the vascularization of endothelial cells (ECs), enhance vascular-osteo communication, and then boost the osteogenic differentiation of bone marrow stem cells (BMSCs), evidenced in mouse critical-sized cranial model. Moreover, we found that PSP serves as a 'priming' agent, activating the body's innate ability to produce Osteolectin (Oln) - prompting ECs to release small extracellular vesicles (sEVs) enriched with Oln to facilitate bone formation. In summary, our study established a precise and efficient composite model of DL and NLP to screen bioactive peptides, opening an avenue for the development of various peptide-based therapeutic strategies applicable to a broader range of diseases.
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Affiliation(s)
- Yu Chen
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stom, Shanghai, 200011, China
| | - Long Chen
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, China
| | - Jinyang Wu
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stom, Shanghai, 200011, China
| | - Xiaofeng Xu
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stom, Shanghai, 200011, China
| | - Chengshuai Yang
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stom, Shanghai, 200011, China
| | - Yong Zhang
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stom, Shanghai, 200011, China
| | - Xinrong Chen
- Academy for Engineering and Technology, Fudan University, Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Shanghai, 200000, China
| | - Kaili Lin
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stom, Shanghai, 200011, China
| | - Shilei Zhang
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stom, Shanghai, 200011, China
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16
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You Q, Yu J, Pan R, Feng J, Guo H, Liu B. Decoding the regulatory roles of circular RNAs in cardiac fibrosis. Noncoding RNA Res 2025; 11:115-130. [PMID: 39759175 PMCID: PMC11697406 DOI: 10.1016/j.ncrna.2024.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 09/04/2024] [Accepted: 11/28/2024] [Indexed: 01/07/2025] Open
Abstract
Cardiovascular diseases (CVDs) are the primary cause of death globally. The evolution of nearly all types of CVDs is characterized by a common theme: the emergence of cardiac fibrosis. The precise mechanisms that trigger cardiac fibrosis are still not completely understood. In recent years, a type of non-coding regulatory RNA molecule known as circular RNAs (circRNAs) has been reported. These molecules are produced during back splicing and possess significant biological capabilities, such as regulating microRNA activity, serving as protein scaffolds and recruiters, competing with mRNA, forming circR-loop structures to modulate transcription, and translating polypeptides. Furthermore, circRNAs exhibit a substantial abundance, notable stability, and specificity of tissues, cells, and time, endowing them with the potential as biomarkers, therapeutic targets, and therapeutic agents. CircRNAs have garnered growing interest in the field of CVDs. Recent investigations into the involvement of circRNAs in cardiac fibrosis have yielded encouraging findings. This study aims to provide a concise overview of the existing knowledge about the regulatory roles of circRNAs in cardiac fibrosis.
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Affiliation(s)
| | | | - Runfang Pan
- Department of Anatomy, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Jiaming Feng
- Department of Anatomy, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Haidong Guo
- Department of Anatomy, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Baonian Liu
- Department of Anatomy, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
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17
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Araujo NA, Veloso M, Pouchucq L. Hydrodynamic characterization of the FtsZ protein from Escherichia coli demonstrates the presence of linear and lateral trimers. Anal Biochem 2025; 699:115766. [PMID: 39788364 DOI: 10.1016/j.ab.2025.115766] [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: 11/08/2024] [Revised: 12/30/2024] [Accepted: 01/07/2025] [Indexed: 01/12/2025]
Abstract
FtsZ is a bacterial protein that plays a crucial role in cytokinesis by forming the Z-ring. This ring acts as a scaffold to recruit other division proteins and guide the synthesis of septal peptidoglycan, which leads to cell constriction. In its native state, the FtsZ protein from Escherichia coli (EcFtsZ) is a multi-oligomer comprising dimers, trimers, tetramers, and hexamers in a dynamic self-association equilibrium depending on its concentration. This study employed classical methods of analytical biochemistry that included native polyacrylamide gel electrophoresis, size-exclusion chromatography, sedimentation through sucrose gradients, and chemical cross-linking with formaldehyde to characterize the EcFtsZ. The dimers, trimers, and tetramers are the most prevalent oligomers of the EcFtsZ protein; however, the trimer has been understudied compared to the dimer. In this study, we characterized uncross-linked trimers by exclusion chromatography and crosslinked trimers by sedimentation. The results of size-exclusion chromatography demonstrated that the uncross-linked trimer of EcFtsZ has a mass of 128.8 kDa and a frictional ratio f/fo of 1.96, which coincides with the theoretical frictional ratio of 1.80 for a linear trimer. The EcFtsZ protein treated with formaldehyde resulted in a polypeptide band of 128 kDa recognized by anti-FtsZ antibodies and a frictional ratio Smax/S20,w equal to 1.95, which agrees with the theoretical calculation of the frictional ratio of a lateral trimer. The protein-protein interaction prediction program (PEPPI) identified a contact site between subunits in the C-terminal linker region of the EcFtsZ protein, which has the potential to interfere with the recognition of the C-terminal linker by the ClpX(P) protease.
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Affiliation(s)
- Nelson A Araujo
- Laboratorio de Biología Estructural y Molecular BEM, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425 Ñuñoa, Santiago, 7800003, Chile.
| | - Marcelo Veloso
- Laboratorio de Biología Estructural y Molecular BEM, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425 Ñuñoa, Santiago, 7800003, Chile
| | - Luis Pouchucq
- Laboratorio de Biología Estructural y Molecular BEM, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425 Ñuñoa, Santiago, 7800003, Chile; Laboratorio de Biotecnología Vegetal y Ambiental Aplicada, Universidad Tecnológica Metropolitana, Santiago, Chile
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18
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Ibrahim S, Khan MU, Noreen S, Firdous S, Khurram I, Rehman R, Javed MA, Ali Q. Advancing brain tumor therapy: unveiling the potential of PROTACs for targeted protein degradation. Cytotechnology 2025; 77:54. [PMID: 39897109 PMCID: PMC11785894 DOI: 10.1007/s10616-025-00716-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 01/14/2025] [Indexed: 02/04/2025] Open
Abstract
The long-term treatment of malignancies, particularly brain tumors, is challenged by abnormal protein expression and drug resistance. In terms of potency, selectivity, and overcoming drug resistance, Proteolysis Targeting Chimeras (PROTACs), a cutting-edge method used to selectively degrade target proteins, beats traditional inhibitors. This review summarizes recent research on using PROTACs as a therapeutic strategy for brain tumors, focusing on their mechanism, benefits, limitations, and the need for optimization. The review draws from a comprehensive search of peer-reviewed literature, scientific databases, and clinical trial databases. Articles published up to the knowledge cutoff date up to 14 April 2023 were included. Inclusion criteria covered PROTAC-based brain tumor therapies, including preclinical and early clinical studies, with no restrictions on design or publication type. We included studies using in vitro, in vivo brain tumor models, and human subjects. Eligible treatments involved PROTACs targeting proteins linked to brain tumor progression. We evaluated the selected studies for methodology, including design, sample size, and data analysis techniques. A narrative synthesis summarized key outcomes and trends in PROTAC-based brain tumor therapy. Recent research shows PROTACs selectively degrade brain tumor-related proteins with minimal off-target effects. They offer enhanced potency, selectivity, and the ability to combat resistance compared to traditional inhibitors. PROTACs hold promise for brain tumor treatment offering advantages over traditional inhibitors, but more research is needed to refine their mechanisms, efficacy, and safety. Larger-scale trials and translational studies are essential for assessing their clinical utility.
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Affiliation(s)
- Saooda Ibrahim
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Umer Khan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Saadia Noreen
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Safia Firdous
- Faculty of Rehabilitation and Allied Health Sciences, Riphah International University, Lahore, Pakistan
| | - Iqra Khurram
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Raima Rehman
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Arshad Javed
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Qurban Ali
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
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19
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Tiwari M, Sodhi M, Chanda D, Kataria RS, Niranjan SK, Singh I, Bharti VK, Iqbal M, Rabgais S, Amarjeet, Vivek P, Kumari P, Mukesh M. Deciphering genomic basis of unique adaptation of Ladakhi cattle to Trans-Himalayan high-altitude region of Leh-Ladakh in India. Gene 2025; 942:149251. [PMID: 39809370 DOI: 10.1016/j.gene.2025.149251] [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: 07/11/2024] [Revised: 01/02/2025] [Accepted: 01/10/2025] [Indexed: 01/16/2025]
Abstract
In this study, whole genome sequence data of Ladakhi cattle from high altitude region of Leh-Ladakh and Sahiwal cattle from arid, semi-arid tropical region were compared. To gain a deeper understanding of the selective footprints in the genomes of Ladakhi and Sahiwal cattle, two strategies namely run of homozygosity (ROH), and fixation index (FST) were employed. A total of 975 and 1189 ROH regions were identified in Ladakhi and Sahiwal cattle, respectively. Several genes associated with high-altitude adaptation were enriched in many of the ROH hot spots in genome of Ladakhi cattle such as; HIF1A, VEGFA, VEGFC, EPHB1, ZEB1, CAV3, TEK, SENP2, GATA6, RAD51 and ADAMTSL4 etc.. The FST value of 0.32 also indicated strong genetic differentiation between Ladakhi and Sahiwal cattle. A total of 3616 genomic regions were identified to be under selection in the two cattle breeds. The FST selection signature analysis led to identification of several genes such as HIF1A, VEGFC, ZEB1, SOD1, EGLN3, EPAS1, ZNF, DYSF, ADAM, SENP2, MMP16, and CDK2 etc., that could be associated with high altitude adaptation in Ladakhi cattle. Additionally, several signalling pathways found in Ladakhi cattle like HIF1A, VEGF, DNA repair, and angiogenesis, which are associated with adaptation to high-altitude hypoxic environments. The phylogenetic, PCA and admixture analysis separated the individuals of Ladakhi and Sahiwal cattle according to their geographic origin. In the present study, the WGS data has helped to identify key genes and genic regions that contribute to high altitude adaptation in Ladakhi cattle.
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Affiliation(s)
- Manish Tiwari
- ICAR-National Bureau of Animal Genetic Resources (NBAGR), Karnal, Haryana, India
| | - Monika Sodhi
- ICAR-National Bureau of Animal Genetic Resources (NBAGR), Karnal, Haryana, India
| | - Divya Chanda
- ICAR-National Bureau of Animal Genetic Resources (NBAGR), Karnal, Haryana, India
| | - Ranjit S Kataria
- ICAR-National Bureau of Animal Genetic Resources (NBAGR), Karnal, Haryana, India
| | - Saket K Niranjan
- ICAR-National Bureau of Animal Genetic Resources (NBAGR), Karnal, Haryana, India
| | - Inderpal Singh
- ICAR-National Bureau of Animal Genetic Resources (NBAGR), Karnal, Haryana, India
| | - Vijay K Bharti
- DRDO-Defense Institute of High-Altitude Research (DIHAR), Leh, India
| | - M Iqbal
- Animal Husbandry Department, Leh, UT Ladakh, India
| | | | - Amarjeet
- ICAR-National Bureau of Animal Genetic Resources (NBAGR), Karnal, Haryana, India
| | - Prince Vivek
- ICAR-National Bureau of Animal Genetic Resources (NBAGR), Karnal, Haryana, India
| | - Parvesh Kumari
- ICAR-National Bureau of Animal Genetic Resources (NBAGR), Karnal, Haryana, India
| | - Manishi Mukesh
- ICAR-National Bureau of Animal Genetic Resources (NBAGR), Karnal, Haryana, India.
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Miguel-Hidalgo JJ, Kelly I, Rajkowska G. Paranode length in the prefrontal cortex of subjects with major depression and rats under chronic unpredictable stress. J Affect Disord 2025; 373:158-165. [PMID: 39743147 PMCID: PMC11794008 DOI: 10.1016/j.jad.2024.12.106] [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 |