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Pham DL, Gillette AA, Riendeau J, Wiech K, Guzman EC, Datta R, Skala MC. Perspectives on label-free microscopy of heterogeneous and dynamic biological systems. JOURNAL OF BIOMEDICAL OPTICS 2025; 29:S22702. [PMID: 38434231 PMCID: PMC10903072 DOI: 10.1117/1.jbo.29.s2.s22702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/22/2023] [Accepted: 12/14/2023] [Indexed: 03/05/2024]
Abstract
Significance Advancements in label-free microscopy could provide real-time, non-invasive imaging with unique sources of contrast and automated standardized analysis to characterize heterogeneous and dynamic biological processes. These tools would overcome challenges with widely used methods that are destructive (e.g., histology, flow cytometry) or lack cellular resolution (e.g., plate-based assays, whole animal bioluminescence imaging). Aim This perspective aims to (1) justify the need for label-free microscopy to track heterogeneous cellular functions over time and space within unperturbed systems and (2) recommend improvements regarding instrumentation, image analysis, and image interpretation to address these needs. Approach Three key research areas (cancer research, autoimmune disease, and tissue and cell engineering) are considered to support the need for label-free microscopy to characterize heterogeneity and dynamics within biological systems. Based on the strengths (e.g., multiple sources of molecular contrast, non-invasive monitoring) and weaknesses (e.g., imaging depth, image interpretation) of several label-free microscopy modalities, improvements for future imaging systems are recommended. Conclusion Improvements in instrumentation including strategies that increase resolution and imaging speed, standardization and centralization of image analysis tools, and robust data validation and interpretation will expand the applications of label-free microscopy to study heterogeneous and dynamic biological systems.
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Affiliation(s)
- Dan L. Pham
- University of Wisconsin—Madison, Department of Biomedical Engineering, Madison, Wisconsin, United States
| | | | | | - Kasia Wiech
- University of Wisconsin—Madison, Department of Biomedical Engineering, Madison, Wisconsin, United States
| | | | - Rupsa Datta
- Morgridge Institute for Research, Madison, Wisconsin, United States
| | - Melissa C. Skala
- University of Wisconsin—Madison, Department of Biomedical Engineering, Madison, Wisconsin, United States
- Morgridge Institute for Research, Madison, Wisconsin, United States
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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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Ma C, Rytel K, Chen Y, Sidransky E. New glucocerebrosidase antibodies can advance research in the field of neurodegenerative disorders. Neural Regen Res 2025; 20:1085-1086. [PMID: 38989943 DOI: 10.4103/nrr.nrr-d-24-00131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/26/2024] [Indexed: 07/12/2024] Open
Affiliation(s)
- Charis Ma
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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4
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Luo W, Xu C, Li L, Ji Y, Wang Y, Li Y, Ye Y. Perfluoropentane-based oxygen-loaded nanodroplets reduce microglial activation through metabolic reprogramming. Neural Regen Res 2025; 20:1178-1191. [PMID: 38989955 DOI: 10.4103/nrr.nrr-d-23-01299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 02/05/2024] [Indexed: 07/12/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202504000-00032/figure1/v/2024-07-06T104127Z/r/image-tiff Microglia, the primary immune cells within the brain, have gained recognition as a promising therapeutic target for managing neurodegenerative diseases within the central nervous system, including Parkinson's disease. Nanoscale perfluorocarbon droplets have been reported to not only possess a high oxygen-carrying capacity, but also exhibit remarkable anti-inflammatory properties. However, the role of perfluoropentane in microglia-mediated central inflammatory reactions remains poorly understood. In this study, we developed perfluoropentane-based oxygen-loaded nanodroplets (PFP-OLNDs) and found that pretreatment with these droplets suppressed the lipopolysaccharide-induced activation of M1-type microglia in vitro and in vivo, and suppressed microglial activation in a mouse model of Parkinson's disease. Microglial suppression led to a reduction in the inflammatory response, oxidative stress, and cell migration capacity in vitro. Consequently, the neurotoxic effects were mitigated, which alleviated neuronal degeneration. Additionally, ultrahigh-performance liquid chromatography-tandem mass spectrometry showed that the anti-inflammatory effects of PFP-OLNDs mainly resulted from the modulation of microglial metabolic reprogramming. We further showed that PFP-OLNDs regulated microglial metabolic reprogramming through the AKT-mTOR-HIF-1α pathway. Collectively, our findings suggest that the novel PFP-OLNDs constructed in this study alleviate microglia-mediated central inflammatory reactions through metabolic reprogramming.
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Affiliation(s)
- Wanxian Luo
- Department of Medicine Ultrasonics, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Chuanhui Xu
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Linxi Li
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Yunxiang Ji
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Yezhong Wang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Yingjia Li
- Department of Medicine Ultrasonics, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Yongyi Ye
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
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Tang X, Zheng N, Lin Q, You Y, Gong Z, Zhuang Y, Wu J, Wang Y, Huang H, Ke J, Chen F. Hypoxia-preconditioned bone marrow-derived mesenchymal stem cells protect neurons from cardiac arrest-induced pyroptosis. Neural Regen Res 2025; 20:1103-1123. [PMID: 38845218 DOI: 10.4103/nrr.nrr-d-23-01922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 04/28/2024] [Indexed: 07/12/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202504000-00027/figure1/v/2024-07-06T104127Z/r/image-tiff Cardiac arrest can lead to severe neurological impairment as a result of inflammation, mitochondrial dysfunction, and post-cardiopulmonary resuscitation neurological damage. Hypoxic preconditioning has been shown to improve migration and survival of bone marrow-derived mesenchymal stem cells and reduce pyroptosis after cardiac arrest, but the specific mechanisms by which hypoxia-preconditioned bone marrow-derived mesenchymal stem cells protect against brain injury after cardiac arrest are unknown. To this end, we established an in vitro co-culture model of bone marrow-derived mesenchymal stem cells and oxygen-glucose deprived primary neurons and found that hypoxic preconditioning enhanced the protective effect of bone marrow stromal stem cells against neuronal pyroptosis, possibly through inhibition of the MAPK and nuclear factor κB pathways. Subsequently, we transplanted hypoxia-preconditioned bone marrow-derived mesenchymal stem cells into the lateral ventricle after the return of spontaneous circulation in an 8-minute cardiac arrest rat model induced by asphyxia. The results showed that hypoxia-preconditioned bone marrow-derived mesenchymal stem cells significantly reduced cardiac arrest-induced neuronal pyroptosis, oxidative stress, and mitochondrial damage, whereas knockdown of the liver isoform of phosphofructokinase in bone marrow-derived mesenchymal stem cells inhibited these effects. To conclude, hypoxia-preconditioned bone marrow-derived mesenchymal stem cells offer a promising therapeutic approach for neuronal injury following cardiac arrest, and their beneficial effects are potentially associated with increased expression of the liver isoform of phosphofructokinase following hypoxic preconditioning.
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Affiliation(s)
- Xiahong Tang
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou, Fujian Province, China
- Department of Emergency, Fujian Provincial Hospital, Fuzhou, Fujian Province, China
- Fujian Provincial Key Laboratory of Emergency Medicine, Fuzhou, Fujian Province, China
| | - Nan Zheng
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou, Fujian Province, China
- Department of Emergency, Fujian Provincial Hospital, Fuzhou, Fujian Province, China
- Fujian Provincial Key Laboratory of Emergency Medicine, Fuzhou, Fujian Province, China
| | - Qingming Lin
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou, Fujian Province, China
- Department of Emergency, Fujian Provincial Hospital, Fuzhou, Fujian Province, China
- Fujian Provincial Key Laboratory of Emergency Medicine, Fuzhou, Fujian Province, China
| | - Yan You
- The Second Department of Intensive Care Unit, Fujian Provincial Hospital South Branch, Fuzhou, Fujian Province, China
| | - Zheng Gong
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou, Fujian Province, China
- Department of Emergency, Fujian Provincial Hospital, Fuzhou, Fujian Province, China
- Fujian Provincial Key Laboratory of Emergency Medicine, Fuzhou, Fujian Province, China
| | - Yangping Zhuang
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou, Fujian Province, China
- Department of Emergency, Fujian Provincial Hospital, Fuzhou, Fujian Province, China
- Fujian Provincial Key Laboratory of Emergency Medicine, Fuzhou, Fujian Province, China
| | - Jiali Wu
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou, Fujian Province, China
- Department of Emergency, Fujian Provincial Hospital, Fuzhou, Fujian Province, China
- Fujian Provincial Key Laboratory of Emergency Medicine, Fuzhou, Fujian Province, China
| | - Yu Wang
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou, Fujian Province, China
- Department of Emergency, Fujian Provincial Hospital, Fuzhou, Fujian Province, China
- Fujian Provincial Key Laboratory of Emergency Medicine, Fuzhou, Fujian Province, China
| | - Hanlin Huang
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou, Fujian Province, China
- Department of Emergency, Fujian Provincial Hospital, Fuzhou, Fujian Province, China
- Fujian Provincial Key Laboratory of Emergency Medicine, Fuzhou, Fujian Province, China
| | - Jun Ke
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou, Fujian Province, China
- Department of Emergency, Fujian Provincial Hospital, Fuzhou, Fujian Province, China
- Fujian Provincial Key Laboratory of Emergency Medicine, Fuzhou, Fujian Province, China
| | - Feng Chen
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou, Fujian Province, China
- Department of Emergency, Fujian Provincial Hospital, Fuzhou, Fujian Province, China
- Fujian Provincial Key Laboratory of Emergency Medicine, Fuzhou, Fujian Province, China
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Wang P, Bi Y, Li M, Chen J, Wang Z, Wen H, Zhou M, Luo M, Zhang W. Cortico-striatal gamma oscillations are modulated by dopamine D3 receptors in dyskinetic rats. Neural Regen Res 2025; 20:1164-1177. [PMID: 38989954 DOI: 10.4103/nrr.nrr-d-23-01240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/16/2024] [Indexed: 07/12/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202504000-00031/figure1/v/2024-07-06T104127Z/r/image-tiff Long-term levodopa administration can lead to the development of levodopa-induced dyskinesia. Gamma oscillations are a widely recognized hallmark of abnormal neural electrical activity in levodopa-induced dyskinesia. Currently, studies have reported increased oscillation power in cases of levodopa-induced dyskinesia. However, little is known about how the other electrophysiological parameters of gamma oscillations are altered in levodopa-induced dyskinesia. Furthermore, the role of the dopamine D3 receptor, which is implicated in levodopa-induced dyskinesia, in movement disorder-related changes in neural oscillations is unclear. We found that the cortico-striatal functional connectivity of beta oscillations was enhanced in a model of Parkinson's disease. Furthermore, levodopa application enhanced cortical gamma oscillations in cortico-striatal projections and cortical gamma aperiodic components, as well as bidirectional primary motor cortex (M1) ↔ dorsolateral striatum gamma flow. Administration of PD128907 (a selective dopamine D3 receptor agonist) induced dyskinesia and excessive gamma oscillations with a bidirectional M1 ↔ dorsolateral striatum flow. However, administration of PG01037 (a selective dopamine D3 receptor antagonist) attenuated dyskinesia, suppressed gamma oscillations and cortical gamma aperiodic components, and decreased gamma causality in the M1 → dorsolateral striatum direction. These findings suggest that the dopamine D3 receptor plays a role in dyskinesia-related oscillatory activity, and that it has potential as a therapeutic target for levodopa-induced dyskinesia.
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Affiliation(s)
- Pengfei Wang
- Neurosurgery Center, Department of Pediatric Neurosurgery, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
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7
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Chen J, Chen J, Yu C, Xia K, Yang B, Wang R, Li Y, Shi K, Zhang Y, Xu H, Zhang X, Wang J, Chen Q, Liang C. Metabolic reprogramming: a new option for the treatment of spinal cord injury. Neural Regen Res 2025; 20:1042-1057. [PMID: 38989936 DOI: 10.4103/nrr.nrr-d-23-01604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 02/27/2024] [Indexed: 07/12/2024] Open
Abstract
Spinal cord injuries impose a notably economic burden on society, mainly because of the severe after-effects they cause. Despite the ongoing development of various therapies for spinal cord injuries, their effectiveness remains unsatisfactory. However, a deeper understanding of metabolism has opened up a new therapeutic opportunity in the form of metabolic reprogramming. In this review, we explore the metabolic changes that occur during spinal cord injuries, their consequences, and the therapeutic tools available for metabolic reprogramming. Normal spinal cord metabolism is characterized by independent cellular metabolism and intercellular metabolic coupling. However, spinal cord injury results in metabolic disorders that include disturbances in glucose metabolism, lipid metabolism, and mitochondrial dysfunction. These metabolic disturbances lead to corresponding pathological changes, including the failure of axonal regeneration, the accumulation of scarring, and the activation of microglia. To rescue spinal cord injury at the metabolic level, potential metabolic reprogramming approaches have emerged, including replenishing metabolic substrates, reconstituting metabolic couplings, and targeting mitochondrial therapies to alter cell fate. The available evidence suggests that metabolic reprogramming holds great promise as a next-generation approach for the treatment of spinal cord injury. To further advance the metabolic treatment of the spinal cord injury, future efforts should focus on a deeper understanding of neurometabolism, the development of more advanced metabolomics technologies, and the design of highly effective metabolic interventions.
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Affiliation(s)
- Jiangjie Chen
- Department of Orthopedics, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- Orthopedics Research Institute of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou, Zhejiang Province, China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Jinyang Chen
- Department of Orthopedics, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- Orthopedics Research Institute of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou, Zhejiang Province, China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Chao Yu
- Department of Orthopedics, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- Orthopedics Research Institute of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou, Zhejiang Province, China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Kaishun Xia
- Department of Orthopedics, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- Orthopedics Research Institute of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou, Zhejiang Province, China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Biao Yang
- Qiandongnan Prefecture People's Hospital, Kaili, Guizhou Province, China
| | - Ronghao Wang
- Department of Orthopedics, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- Orthopedics Research Institute of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou, Zhejiang Province, China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Yi Li
- Department of Orthopedics, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- Orthopedics Research Institute of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou, Zhejiang Province, China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Kesi Shi
- Department of Orthopedics, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- Orthopedics Research Institute of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou, Zhejiang Province, China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Yuang Zhang
- Department of Orthopedics, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- Orthopedics Research Institute of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou, Zhejiang Province, China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Haibin Xu
- Department of Orthopedics, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- Orthopedics Research Institute of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou, Zhejiang Province, China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Xuesong Zhang
- Department of Orthopedics, Fourth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Jingkai Wang
- Department of Orthopedics, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- Orthopedics Research Institute of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou, Zhejiang Province, China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Qixin Chen
- Department of Orthopedics, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- Orthopedics Research Institute of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou, Zhejiang Province, China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Chengzhen Liang
- Department of Orthopedics, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- Orthopedics Research Institute of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou, Zhejiang Province, China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou, Zhejiang Province, China
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Yin Z, Kang J, Cheng X, Gao H, Huo S, Xu H. Investigating Müller glia reprogramming in mice: a retrospective of the last decade, and a look to the future. Neural Regen Res 2025; 20:946-959. [PMID: 38989930 DOI: 10.4103/nrr.nrr-d-23-01612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/05/2024] [Indexed: 07/12/2024] Open
Abstract
Müller glia, as prominent glial cells within the retina, plays a significant role in maintaining retinal homeostasis in both healthy and diseased states. In lower vertebrates like zebrafish, these cells assume responsibility for spontaneous retinal regeneration, wherein endogenous Müller glia undergo proliferation, transform into Müller glia-derived progenitor cells, and subsequently regenerate the entire retina with restored functionality. Conversely, Müller glia in the mouse and human retina exhibit limited neural reprogramming. Müller glia reprogramming is thus a promising strategy for treating neurodegenerative ocular disorders. Müller glia reprogramming in mice has been accomplished with remarkable success, through various technologies. Advancements in molecular, genetic, epigenetic, morphological, and physiological evaluations have made it easier to document and investigate the Müller glia programming process in mice. Nevertheless, there remain issues that hinder improving reprogramming efficiency and maturity. Thus, understanding the reprogramming mechanism is crucial toward exploring factors that will improve Müller glia reprogramming efficiency, and for developing novel Müller glia reprogramming strategies. This review describes recent progress in relatively successful Müller glia reprogramming strategies. It also provides a basis for developing new Müller glia reprogramming strategies in mice, including epigenetic remodeling, metabolic modulation, immune regulation, chemical small-molecules regulation, extracellular matrix remodeling, and cell-cell fusion, to achieve Müller glia reprogramming in mice.
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Affiliation(s)
- Zhiyuan Yin
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Southwest Eye Hospital, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
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Jiao D, Xu L, Gu Z, Yan H, Shen D, Gu X. Pathogenesis, diagnosis, and treatment of epilepsy: electromagnetic stimulation-mediated neuromodulation therapy and new technologies. Neural Regen Res 2025; 20:917-935. [PMID: 38989927 DOI: 10.4103/nrr.nrr-d-23-01444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 01/18/2024] [Indexed: 07/12/2024] Open
Abstract
Epilepsy is a severe, relapsing, and multifactorial neurological disorder. Studies regarding the accurate diagnosis, prognosis, and in-depth pathogenesis are crucial for the precise and effective treatment of epilepsy. The pathogenesis of epilepsy is complex and involves alterations in variables such as gene expression, protein expression, ion channel activity, energy metabolites, and gut microbiota composition. Satisfactory results are lacking for conventional treatments for epilepsy. Surgical resection of lesions, drug therapy, and non-drug interventions are mainly used in clinical practice to treat pain associated with epilepsy. Non-pharmacological treatments, such as a ketogenic diet, gene therapy for nerve regeneration, and neural regulation, are currently areas of research focus. This review provides a comprehensive overview of the pathogenesis, diagnostic methods, and treatments of epilepsy. It also elaborates on the theoretical basis, treatment modes, and effects of invasive nerve stimulation in neurotherapy, including percutaneous vagus nerve stimulation, deep brain electrical stimulation, repetitive nerve electrical stimulation, in addition to non-invasive transcranial magnetic stimulation and transcranial direct current stimulation. Numerous studies have shown that electromagnetic stimulation-mediated neuromodulation therapy can markedly improve neurological function and reduce the frequency of epileptic seizures. Additionally, many new technologies for the diagnosis and treatment of epilepsy are being explored. However, current research is mainly focused on analyzing patients' clinical manifestations and exploring relevant diagnostic and treatment methods to study the pathogenesis at a molecular level, which has led to a lack of consensus regarding the mechanisms related to the disease.
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Affiliation(s)
- Dian Jiao
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Lai Xu
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Zhen Gu
- Key Laboratory of Advanced Drug Delivery Systems of Zhejiang Province, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Hua Yan
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Dingding Shen
- Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Xiaosong Gu
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
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10
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Chen Y, Fan Z, Luo Z, Kang X, Wan R, Li F, Lin W, Han Z, Qi B, Lin J, Sun Y, Huang J, Xu Y, Chen S. Impacts of Nutlin-3a and exercise on murine double minute 2-enriched glioma treatment. Neural Regen Res 2025; 20:1135-1152. [PMID: 38989952 DOI: 10.4103/nrr.nrr-d-23-00875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 12/21/2023] [Indexed: 07/12/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202504000-00029/figure1/v/2024-07-06T104127Z/r/image-tiff Recent research has demonstrated the impact of physical activity on the prognosis of glioma patients, with evidence suggesting exercise may reduce mortality risks and aid neural regeneration. The role of the small ubiquitin-like modifier (SUMO) protein, especially post-exercise, in cancer progression, is gaining attention, as are the potential anti-cancer effects of SUMOylation. We used machine learning to create the exercise and SUMO-related gene signature (ESLRS). This signature shows how physical activity might help improve the outlook for low-grade glioma and other cancers. We demonstrated the prognostic and immunotherapeutic significance of ESLRS markers, specifically highlighting how murine double minute 2 (MDM2), a component of the ESLRS, can be targeted by nutlin-3. This underscores the intricate relationship between natural compounds such as nutlin-3 and immune regulation. Using comprehensive CRISPR screening, we validated the effects of specific ESLRS genes on low-grade glioma progression. We also revealed insights into the effectiveness of Nutlin-3a as a potent MDM2 inhibitor through molecular docking and dynamic simulation. Nutlin-3a inhibited glioma cell proliferation and activated the p53 pathway. Its efficacy decreased with MDM2 overexpression, and this was reversed by Nutlin-3a or exercise. Experiments using a low-grade glioma mouse model highlighted the effect of physical activity on oxidative stress and molecular pathway regulation. Notably, both physical exercise and Nutlin-3a administration improved physical function in mice bearing tumors derived from MDM2-overexpressing cells. These results suggest the potential for Nutlin-3a, an MDM2 inhibitor, with physical exercise as a therapeutic approach for glioma management. Our research also supports the use of natural products for therapy and sheds light on the interaction of exercise, natural products, and immune regulation in cancer treatment.
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Affiliation(s)
- Yisheng Chen
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhongcheng Fan
- Department of Orthopedic Surgery, Hainan Province Clinical Medical Center, Haikou Affiliated Hospital of Central South University Xiangya School of Medicine, Haikou, Hainan Province, China
| | - Zhiwen Luo
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Xueran Kang
- Department of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Renwen Wan
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Fangqi Li
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Weiwei Lin
- Department of Neurosurgery, Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Zhihua Han
- Department of Orthopedics, Shanghai General Hospital, School of Medicine Shanghai Jiao Tong University, Shanghai, China
| | - Beijie Qi
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Jinrong Lin
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Yaying Sun
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiebin Huang
- Department of Infectious Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yuzhen Xu
- Department of Rehabilitation, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong Province, China
| | - Shiyi Chen
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
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11
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Mellado S, Morillo-Bargues MJ, Perpiñá-Clérigues C, García-García F, Moreno-Manzano V, Guerri C, Pascual M. The emerging role of mesenchymal stem cell-derived extracellular vesicles to ameliorate hippocampal NLRP3 inflammation induced by binge-like ethanol treatment in adolescence. Neural Regen Res 2025; 20:1153-1163. [PMID: 38989953 DOI: 10.4103/nrr.nrr-d-23-01397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 11/13/2023] [Indexed: 07/12/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202504000-00030/figure1/v/2024-07-06T104127Z/r/image-tiff Our previous studies have reported that activation of the NLRP3 (NOD-, LRR- and pyrin domain-containing protein 3)-inflammasome complex in ethanol-treated astrocytes and chronic alcohol-fed mice could be associated with neuroinflammation and brain damage. Mesenchymal stem cell-derived extracellular vesicles (MSC-EVs) have been shown to restore the neuroinflammatory response, along with myelin and synaptic structural alterations in the prefrontal cortex, and alleviate cognitive and memory dysfunctions induced by binge-like ethanol treatment in adolescent mice. Considering the therapeutic role of the molecules contained in mesenchymal stem cell-derived extracellular vesicles, the present study analyzed whether the administration of mesenchymal stem cell-derived extracellular vesicles isolated from adipose tissue, which inhibited the activation of the NLRP3 inflammasome, was capable of reducing hippocampal neuroinflammation in adolescent mice treated with binge drinking. We demonstrated that the administration of mesenchymal stem cell-derived extracellular vesicles ameliorated the activation of the hippocampal NLRP3 inflammasome complex and other NLRs inflammasomes (e.g., pyrin domain-containing 1, caspase recruitment domain-containing 4, and absent in melanoma 2, as well as the alterations in inflammatory genes (interleukin-1β, interleukin-18, inducible nitric oxide synthase, nuclear factor-kappa B, monocyte chemoattractant protein-1, and C-X3-C motif chemokine ligand 1) and miRNAs (miR-21a-5p, miR-146a-5p, and miR-141-5p) induced by binge-like ethanol treatment in adolescent mice. Bioinformatic analysis further revealed the involvement of miR-21a-5p and miR-146a-5p with inflammatory target genes and NOD-like receptor signaling pathways. Taken together, these findings provide novel evidence of the therapeutic potential of MSC-derived EVs to ameliorate the hippocampal neuroinflammatory response associated with NLRP3 inflammasome activation induced by binge drinking in adolescence.
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Affiliation(s)
- Susana Mellado
- Department of Physiology, School of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | | | - Carla Perpiñá-Clérigues
- Department of Physiology, School of Medicine and Dentistry, University of Valencia, Valencia, Spain
- Bioinformatics and Biostatistics Unit, Príncipe Felipe Research Center, Valencia, Spain
| | | | - Victoria Moreno-Manzano
- Neuronal and Tissue Regeneration Laboratory, Príncipe Felipe Research Center, Valencia, Spain
| | - Consuelo Guerri
- Department of Physiology, School of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - María Pascual
- Department of Physiology, School of Medicine and Dentistry, University of Valencia, Valencia, Spain
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12
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Wang J, Zhang B, Li L, Tang X, Zeng J, Song Y, Xu C, Zhao K, Liu G, Lu Y, Li X, Shu K. Repetitive traumatic brain injury-induced complement C1-related inflammation impairs long-term hippocampal neurogenesis. Neural Regen Res 2025; 20:821-835. [PMID: 38886955 DOI: 10.4103/nrr.nrr-d-23-01446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/21/2023] [Indexed: 06/20/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202503000-00027/figure1/v/2024-06-17T092413Z/r/image-tiff Repetitive traumatic brain injury impacts adult neurogenesis in the hippocampal dentate gyrus, leading to long-term cognitive impairment. However, the mechanism underlying this neurogenesis impairment remains unknown. In this study, we established a male mouse model of repetitive traumatic brain injury and performed long-term evaluation of neurogenesis of the hippocampal dentate gyrus after repetitive traumatic brain injury. Our results showed that repetitive traumatic brain injury inhibited neural stem cell proliferation and development, delayed neuronal maturation, and reduced the complexity of neuronal dendrites and spines. Mice with repetitive traumatic brain injuryalso showed deficits in spatial memory retrieval. Moreover, following repetitive traumatic brain injury, neuroinflammation was enhanced in the neurogenesis microenvironment where C1q levels were increased, C1q binding protein levels were decreased, and canonical Wnt/β-catenin signaling was downregulated. An inhibitor of C1 reversed the long-term impairment of neurogenesis induced by repetitive traumatic brain injury and improved neurological function. These findings suggest that repetitive traumatic brain injury-induced C1-related inflammation impairs long-term neurogenesis in the dentate gyrus and contributes to spatial memory retrieval dysfunction.
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Affiliation(s)
- Jing Wang
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
- Department of Neurosurgery, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, China
| | - Bing Zhang
- Department of Pathophysiology, School of Basic Medicine and Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
- Institute for Brain Research, Wuhan Center of Brain Science, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Lanfang Li
- Department of Pathophysiology, School of Basic Medicine and Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
- Institute for Brain Research, Wuhan Center of Brain Science, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Xiaomei Tang
- Department of Pathophysiology, School of Basic Medicine and Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
- Institute for Brain Research, Wuhan Center of Brain Science, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Jinyu Zeng
- Department of Pathophysiology, School of Basic Medicine and Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
- Institute for Brain Research, Wuhan Center of Brain Science, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Yige Song
- Department of Pathophysiology, School of Basic Medicine and Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
- Institute for Brain Research, Wuhan Center of Brain Science, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Chao Xu
- Department of Graduate Student, Chongqing Medical University, Chongqing, China
| | - Kai Zhao
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Guoqiang Liu
- Department of Basic Medicine, School of Medical Science, Hubei University for Nationalities, Enshi, Hubei Province, China
| | - Youming Lu
- Department of Pathophysiology, School of Basic Medicine and Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
- Institute for Brain Research, Wuhan Center of Brain Science, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Xinyan Li
- Department of Pathophysiology, School of Basic Medicine and Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
- Institute for Brain Research, Wuhan Center of Brain Science, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
- Department of Anatomy, School of Basic Medicine and Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Kai Shu
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
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13
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An Z, Jiang A, Chen J. Toward understanding the role of genomic repeat elements in neurodegenerative diseases. Neural Regen Res 2025; 20:646-659. [PMID: 38886931 DOI: 10.4103/nrr.nrr-d-23-01568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 03/02/2024] [Indexed: 06/20/2024] Open
Abstract
Neurodegenerative diseases cause great medical and economic burdens for both patients and society; however, the complex molecular mechanisms thereof are not yet well understood. With the development of high-coverage sequencing technology, researchers have started to notice that genomic repeat regions, previously neglected in search of disease culprits, are active contributors to multiple neurodegenerative diseases. In this review, we describe the association between repeat element variants and multiple degenerative diseases through genome-wide association studies and targeted sequencing. We discuss the identification of disease-relevant repeat element variants, further powered by the advancement of long-read sequencing technologies and their related tools, and summarize recent findings in the molecular mechanisms of repeat element variants in brain degeneration, such as those causing transcriptional silencing or RNA-mediated gain of toxic function. Furthermore, we describe how in silico predictions using innovative computational models, such as deep learning language models, could enhance and accelerate our understanding of the functional impact of repeat element variants. Finally, we discuss future directions to advance current findings for a better understanding of neurodegenerative diseases and the clinical applications of genomic repeat elements.
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Affiliation(s)
- Zhengyu An
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Aidi Jiang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Jingqi Chen
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Zhangjiang Fudan International Innovation Center, Shanghai, China
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14
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Huang LY, Zhang YD, Chen J, Fan HD, Wang W, Wang B, Ma JY, Li PP, Pu HW, Guo XY, Shen JG, Qi SH. Maintaining moderate levels of hypochlorous acid promotes neural stem cell proliferation and differentiation in the recovery phase of stroke. Neural Regen Res 2025; 20:845-857. [PMID: 38886957 DOI: 10.4103/1673-5374.392889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 11/23/2023] [Indexed: 06/20/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202503000-00029/figure1/v/2024-06-17T092413Z/r/image-tiff It has been shown clinically that continuous removal of ischemia/reperfusion-induced reactive oxygen species is not conducive to the recovery of late stroke. Indeed, previous studies have shown that excessive increases in hypochlorous acid after stroke can cause severe damage to brain tissue. Our previous studies have found that a small amount of hypochlorous acid still exists in the later stage of stroke, but its specific role and mechanism are currently unclear. To simulate stroke in vivo, a middle cerebral artery occlusion rat model was established, with an oxygen-glucose deprivation/reoxygenation model established in vitro to mimic stroke. We found that in the early stage (within 24 hours) of ischemic stroke, neutrophils produced a large amount of hypochlorous acid, while in the recovery phase (10 days after stroke), microglia were activated and produced a small amount of hypochlorous acid. Further, in acute stroke in rats, hypochlorous acid production was prevented using a hypochlorous acid scavenger, taurine, or myeloperoxidase inhibitor, 4-aminobenzoic acid hydrazide. Our results showed that high levels of hypochlorous acid (200 μM) induced neuronal apoptosis after oxygen/glucose deprivation/reoxygenation. However, in the recovery phase of the middle cerebral artery occlusion model, a moderate level of hypochlorous acid promoted the proliferation and differentiation of neural stem cells into neurons and astrocytes. This suggests that hypochlorous acid plays different roles at different phases of cerebral ischemia/reperfusion injury. Lower levels of hypochlorous acid (5 and 100 μM) promoted nuclear translocation of β-catenin. By transfection of single-site mutation plasmids, we found that hypochlorous acid induced chlorination of the β-catenin tyrosine 30 residue, which promoted nuclear translocation. Altogether, our study indicates that maintaining low levels of hypochlorous acid plays a key role in the recovery of neurological function.
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Affiliation(s)
- Lin-Yan Huang
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Yi-De Zhang
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Jie Chen
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Hai-Di Fan
- School of Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
- Department of Laboratory Medicine, Branch Hospital of Huai'an First People's Hospital, Huai'an, Jiangsu Province, China
| | - Wan Wang
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Bin Wang
- Department of Laboratory Medicine, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Ju-Yun Ma
- School of Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Peng-Peng Li
- Department of Laboratory Medicine, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Hai-Wei Pu
- Department of Laboratory Medicine, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Xin-Yian Guo
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Jian-Gang Shen
- School of Chinese Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Su-Hua Qi
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
- School of Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
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15
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Ding X, Chen C, Zhao H, Dai B, Ye L, Song T, Huang S, Wang J, You T. Inhibiting SHP2 reduces glycolysis, promotes microglial M1 polarization, and alleviates secondary inflammation following spinal cord injury in a mouse model. Neural Regen Res 2025; 20:858-872. [PMID: 38886958 DOI: 10.4103/nrr.nrr-d-23-01925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 04/17/2024] [Indexed: 06/20/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202503000-00030/figure1/v/2024-06-17T092413Z/r/image-tiff Reducing the secondary inflammatory response, which is partly mediated by microglia, is a key focus in the treatment of spinal cord injury. Src homology 2-containing protein tyrosine phosphatase 2 (SHP2), encoded by PTPN11, is widely expressed in the human body and plays a role in inflammation through various mechanisms. Therefore, SHP2 is considered a potential target for the treatment of inflammation-related diseases. However, its role in secondary inflammation after spinal cord injury remains unclear. In this study, SHP2 was found to be abundantly expressed in microglia at the site of spinal cord injury. Inhibition of SHP2 expression using siRNA and SHP2 inhibitors attenuated the microglial inflammatory response in an in vitro lipopolysaccharide-induced model of inflammation. Notably, after treatment with SHP2 inhibitors, mice with spinal cord injury exhibited significantly improved hind limb locomotor function and reduced residual urine volume in the bladder. Subsequent in vitro experiments showed that, in microglia stimulated with lipopolysaccharide, inhibiting SHP2 expression promoted M2 polarization and inhibited M1 polarization. Finally, a co-culture experiment was conducted to assess the effect of microglia treated with SHP2 inhibitors on neuronal cells. The results demonstrated that inflammatory factors produced by microglia promoted neuronal apoptosis, while inhibiting SHP2 expression mitigated these effects. Collectively, our findings suggest that SHP2 enhances secondary inflammation and neuronal damage subsequent to spinal cord injury by modulating microglial phenotype. Therefore, inhibiting SHP2 alleviates the inflammatory response in mice with spinal cord injury and promotes functional recovery postinjury.
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Affiliation(s)
- Xintian Ding
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui Province, China
- Department of Orthopedics, Provincial Hospital Affiliated to Anhui Medical University, Hefei, Anhui Province, China
| | - Chun Chen
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui Province, China
| | - Heng Zhao
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui Province, China
| | - Bin Dai
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui Province, China
| | - Lei Ye
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui Province, China
- Department of Orthopedics, Provincial Hospital Affiliated to Anhui Medical University, Hefei, Anhui Province, China
| | - Tao Song
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui Province, China
| | - Shuai Huang
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui Province, China
| | - Jia Wang
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui Province, China
| | - Tao You
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui Province, China
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16
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Hu B, Wang R, Zhang H, Wang X, Zhou S, Ma B, Luan Y, Wang X, Chen X, Zhang Z, Kang Q. Postnatal development of rat retina: a continuous observation and comparison between the organotypic retinal explant model and in vivo development. Neural Regen Res 2025; 20:900-912. [PMID: 38886961 DOI: 10.4103/nrr.nrr-d-23-01557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/22/2024] [Indexed: 06/20/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202503000-00033/figure1/v/2024-06-17T092413Z/r/image-tiff The organotypic retinal explant culture has been established for more than a decade and offers a range of unique advantages compared with in vivo experiments and cell cultures. However, the lack of systematic and continuous comparison between in vivo retinal development and the organotypic retinal explant culture makes this model controversial in postnatal retinal development studies. Thus, we aimed to verify the feasibility of using this model for postnatal retinal development studies by comparing it with the in vivo retina. In this study, we showed that postnatal retinal explants undergo normal development, and exhibit a consistent structure and timeline with retinas in vivo. Initially, we used SOX2 and PAX6 immunostaining to identify retinal progenitor cells. We then examined cell proliferation and migration by immunostaining with Ki-67 and doublecortin, respectively. Ki-67- and doublecortin-positive cells decreased in both in vivo and explants during postnatal retinogenesis, and exhibited a high degree of similarity in abundance and distribution between groups. Additionally, we used Ceh-10 homeodomain-containing homolog, glutamate-ammonia ligase (glutamine synthetase), neuronal nuclei, and ionized calcium-binding adapter molecule 1 immunostaining to examine the emergence of bipolar cells, Müller glia, mature neurons, and microglia, respectively. The timing and spatial patterns of the emergence of these cell types were remarkably consistent between in vivo and explant retinas. Our study showed that the organotypic retinal explant culture model had a high degree of consistency with the progression of in vivo early postnatal retina development. The findings confirm the accuracy and credibility of this model and support its use for long-term, systematic, and continuous observation.
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Affiliation(s)
- Baoqi Hu
- Department of Ophthalmology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
- Department of Ophthalmology, The First Affiliated Hospital of Northwest University, Xi'an, Shaanxi Province, China
| | - Rui Wang
- Department of Ophthalmology, The First Affiliated Hospital of Northwest University, Xi'an, Shaanxi Province, China
| | - Hanyue Zhang
- Institute of Neurobiology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi Province, China
| | - Xiou Wang
- Department of Ophthalmology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Sijia Zhou
- Department of Ophthalmology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Bo Ma
- Department of Ophthalmology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Yan Luan
- Institute of Neurobiology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi Province, China
| | - Xin Wang
- Department of Ophthalmology, The First Affiliated Hospital of Northwest University, Xi'an, Shaanxi Province, China
| | - Xinlin Chen
- Institute of Neurobiology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi Province, China
| | - Zhichao Zhang
- Institute of Neurobiology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi Province, China
| | - Qianyan Kang
- Department of Ophthalmology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
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17
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Wang C, Cheng F, Han Z, Yan B, Liao P, Yin Z, Ge X, Li D, Zhong R, Liu Q, Chen F, Lei P. Human-induced pluripotent stem cell-derived neural stem cell exosomes improve blood-brain barrier function after intracerebral hemorrhage by activating astrocytes via PI3K/AKT/MCP-1 axis. Neural Regen Res 2025; 20:518-532. [PMID: 38819064 DOI: 10.4103/nrr.nrr-d-23-01889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 03/07/2024] [Indexed: 06/01/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202502000-00029/figure1/v/2024-05-28T214302Z/r/image-tiff Cerebral edema caused by blood-brain barrier injury after intracerebral hemorrhage is an important factor leading to poor prognosis. Human-induced pluripotent stem cell-derived neural stem cell exosomes (hiPSC-NSC-Exos) have shown potential for brain injury repair in central nervous system diseases. In this study, we explored the impact of hiPSC-NSC-Exos on blood-brain barrier preservation and the underlying mechanism. Our results indicated that intranasal delivery of hiPSC-NSC-Exos mitigated neurological deficits, enhanced blood-brain barrier integrity, and reduced leukocyte infiltration in a mouse model of intracerebral hemorrhage. Additionally, hiPSC-NSC-Exos decreased immune cell infiltration, activated astrocytes, and decreased the secretion of inflammatory cytokines like monocyte chemoattractant protein-1, macrophage inflammatory protein-1α, and tumor necrosis factor-α post-intracerebral hemorrhage, thereby improving the inflammatory microenvironment. RNA sequencing indicated that hiPSC-NSC-Exo activated the PI3K/AKT signaling pathway in astrocytes and decreased monocyte chemoattractant protein-1 secretion, thereby improving blood-brain barrier integrity. Treatment with the PI3K/AKT inhibitor LY294002 or the monocyte chemoattractant protein-1 neutralizing agent C1142 abolished these effects. In summary, our findings suggest that hiPSC-NSC-Exos maintains blood-brain barrier integrity, in part by downregulating monocyte chemoattractant protein-1 secretion through activation of the PI3K/AKT signaling pathway in astrocytes.
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Affiliation(s)
- Conglin Wang
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin, China
| | - Fangyuan Cheng
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin, China
| | - Zhaoli Han
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin, China
| | - Bo Yan
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin, China
| | - Pan Liao
- School of Medicine, Nankai University, Tianjin, China
| | - Zhenyu Yin
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin, China
| | - Xintong Ge
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin, China
| | - Dai Li
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin, China
| | - Rongrong Zhong
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin, China
| | - Qiang Liu
- Tianjin Neurological Institute, Tianjin, China
| | | | - Ping Lei
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin, China
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18
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Liu Q, Xie J, Zhou R, Deng J, Nie W, Sun S, Wang H, Shi C. A matrix metalloproteinase-responsive hydrogel system controls angiogenic peptide release for repair of cerebral ischemia/reperfusion injury. Neural Regen Res 2025; 20:503-517. [PMID: 38819063 DOI: 10.4103/nrr.nrr-d-23-01322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/29/2024] [Indexed: 06/01/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202502000-00028/figure1/v/2024-05-28T214302Z/r/image-tiff Vascular endothelial growth factor and its mimic peptide KLTWQELYQLKYKGI (QK) are widely used as the most potent angiogenic factors for the treatment of multiple ischemic diseases. However, conventional topical drug delivery often results in a burst release of the drug, leading to transient retention (inefficacy) and undesirable diffusion (toxicity) in vivo. Therefore, a drug delivery system that responds to changes in the microenvironment of tissue regeneration and controls vascular endothelial growth factor release is crucial to improve the treatment of ischemic stroke. Matrix metalloproteinase-2 (MMP-2) is gradually upregulated after cerebral ischemia. Herein, vascular endothelial growth factor mimic peptide QK was self-assembled with MMP-2-cleaved peptide PLGLAG (TIMP) and customizable peptide amphiphilic (PA) molecules to construct nanofiber hydrogel PA-TIMP-QK. PA-TIMP-QK was found to control the delivery of QK by MMP-2 upregulation after cerebral ischemia/reperfusion and had a similar biological activity with vascular endothelial growth factor in vitro. The results indicated that PA-TIMP-QK promoted neuronal survival, restored local blood circulation, reduced blood-brain barrier permeability, and restored motor function. These findings suggest that the self-assembling nanofiber hydrogel PA-TIMP-QK may provide an intelligent drug delivery system that responds to the microenvironment and promotes regeneration and repair after cerebral ischemia/reperfusion injury.
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Affiliation(s)
- Qi Liu
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Qingdao University, Qingdao, Shandong Province, China
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Jianye Xie
- Department of General Practice, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Runxue Zhou
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Qingdao University, Qingdao, Shandong Province, China
| | - Jin Deng
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Qingdao University, Qingdao, Shandong Province, China
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Weihong Nie
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Qingdao University, Qingdao, Shandong Province, China
| | - Shuwei Sun
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Qingdao University, Qingdao, Shandong Province, China
| | - Haiping Wang
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Chunying Shi
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Qingdao University, Qingdao, Shandong Province, China
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19
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Ren Z, Li T, Liu X, Zhang Z, Chen X, Chen W, Li K, Sheng J. Transforming growth factor-beta 1 enhances discharge activity of cortical neurons. Neural Regen Res 2025; 20:548-556. [PMID: 38819066 DOI: 10.4103/nrr.nrr-d-23-00756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 11/22/2023] [Indexed: 06/01/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202502000-00031/figure1/v/2024-05-28T214302Z/r/image-tiff Transforming growth factor-beta 1 (TGF-β1) has been extensively studied for its pleiotropic effects on central nervous system diseases. The neuroprotective or neurotoxic effects of TGF-β1 in specific brain areas may depend on the pathological process and cell types involved. Voltage-gated sodium channels (VGSCs) are essential ion channels for the generation of action potentials in neurons, and are involved in various neuroexcitation-related diseases. However, the effects of TGF-β1 on the functional properties of VGSCs and firing properties in cortical neurons remain unclear. In this study, we investigated the effects of TGF-β1 on VGSC function and firing properties in primary cortical neurons from mice. We found that TGF-β1 increased VGSC current density in a dose- and time-dependent manner, which was attributable to the upregulation of Nav1.3 expression. Increased VGSC current density and Nav1.3 expression were significantly abolished by preincubation with inhibitors of mitogen-activated protein kinase kinase (PD98059), p38 mitogen-activated protein kinase (SB203580), and Jun NH2-terminal kinase 1/2 inhibitor (SP600125). Interestingly, TGF-β1 significantly increased the firing threshold of action potentials but did not change their firing rate in cortical neurons. These findings suggest that TGF-β1 can increase Nav1.3 expression through activation of the ERK1/2-JNK-MAPK pathway, which leads to a decrease in the firing threshold of action potentials in cortical neurons under pathological conditions. Thus, this contributes to the occurrence and progression of neuroexcitatory-related diseases of the central nervous system.
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Affiliation(s)
- Zhihui Ren
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Tian Li
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Xueer Liu
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Zelin Zhang
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Xiaoxuan Chen
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Weiqiang Chen
- Department of Neurosurgery, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong Province, China
| | - Kangsheng Li
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Jiangtao Sheng
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, Guangdong Province, China
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20
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Feng S, Li J, Liu T, Huang S, Chen X, Liu S, Zhou J, Zhao H, Hong Y. Overexpression of low-density lipoprotein receptor prevents neurotoxic polarization of astrocytes via inhibiting NLRP3 inflammasome activation in experimental ischemic stroke. Neural Regen Res 2025; 20:491-502. [PMID: 38819062 DOI: 10.4103/nrr.nrr-d-23-01263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 02/23/2024] [Indexed: 06/01/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202502000-00027/figure1/v/2024-05-28T214302Z/r/image-tiff Neurotoxic astrocytes are a promising therapeutic target for the attenuation of cerebral ischemia/reperfusion injury. Low-density lipoprotein receptor, a classic cholesterol regulatory receptor, has been found to inhibit NLR family pyrin domain containing protein 3 (NLRP3) inflammasome activation in neurons following ischemic stroke and to suppress the activation of microglia and astrocytes in individuals with Alzheimer's disease. However, little is known about the effects of low-density lipoprotein receptor on astrocytic activation in ischemic stroke. To address this issue in the present study, we examined the mechanisms by which low-density lipoprotein receptor regulates astrocytic polarization in ischemic stroke models. First, we examined low-density lipoprotein receptor expression in astrocytes via immunofluorescence staining and western blotting analysis. We observed significant downregulation of low-density lipoprotein receptor following middle cerebral artery occlusion reperfusion and oxygen-glucose deprivation/reoxygenation. Second, we induced the astrocyte-specific overexpression of low-density lipoprotein receptor using astrocyte-specific adeno-associated virus. Low-density lipoprotein receptor overexpression in astrocytes improved neurological outcomes in middle cerebral artery occlusion mice and reversed neurotoxic astrocytes to create a neuroprotective phenotype. Finally, we found that the overexpression of low-density lipoprotein receptor inhibited NLRP3 inflammasome activation in oxygen-glucose deprivation/reoxygenation injured astrocytes and that the addition of nigericin, an NLRP3 agonist, restored the neurotoxic astrocyte phenotype. These findings suggest that low-density lipoprotein receptor could inhibit the NLRP3-meidiated neurotoxic polarization of astrocytes and that increasing low-density lipoprotein receptor in astrocytes might represent a novel strategy for treating cerebral ischemic stroke.
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Affiliation(s)
- Shuai Feng
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Juanji Li
- Department of Neurology, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province, China
| | - Tingting Liu
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Shiqi Huang
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Xiangliang Chen
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Shen Liu
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Junshan Zhou
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Hongdong Zhao
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Ye Hong
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
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21
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Li T, Xing HM, Qian HD, Gao Q, Xu SL, Ma H, Chi ZL. Small extracellular vesicles derived from human induced pluripotent stem cell-differentiated neural progenitor cells mitigate retinal ganglion cell degeneration in a mouse model of optic nerve injury. Neural Regen Res 2025; 20:587-597. [PMID: 38819069 DOI: 10.4103/nrr.nrr-d-23-01414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 12/29/2023] [Indexed: 06/01/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202502000-00034/figure1/v/2024-05-28T214302Z/r/image-tiff Several studies have found that transplantation of neural progenitor cells (NPCs) promotes the survival of injured neurons. However, a poor integration rate and high risk of tumorigenicity after cell transplantation limits their clinical application. Small extracellular vesicles (sEVs) contain bioactive molecules for neuronal protection and regeneration. Previous studies have shown that stem/progenitor cell-derived sEVs can promote neuronal survival and recovery of neurological function in neurodegenerative eye diseases and other eye diseases. In this study, we intravitreally transplanted sEVs derived from human induced pluripotent stem cells (hiPSCs) and hiPSCs-differentiated NPCs (hiPSC-NPC) in a mouse model of optic nerve crush. Our results show that these intravitreally injected sEVs were ingested by retinal cells, especially those localized in the ganglion cell layer. Treatment with hiPSC-NPC-derived sEVs mitigated optic nerve crush-induced retinal ganglion cell degeneration, and regulated the retinal microenvironment by inhibiting excessive activation of microglia. Component analysis further revealed that hiPSC-NPC derived sEVs transported neuroprotective and anti-inflammatory miRNA cargos to target cells, which had protective effects on RGCs after optic nerve injury. These findings suggest that sEVs derived from hiPSC-NPC are a promising cell-free therapeutic strategy for optic neuropathy.
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Affiliation(s)
- Tong Li
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Hui-Min Xing
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Hai-Dong Qian
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Qiao Gao
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Sheng-Lan Xu
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Hua Ma
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Zai-Long Chi
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
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22
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Lamprea Pineda PA, Demeestere K, Alvarado-Alvarado AA, Devlieghere F, Boon N, Van Langenhove H, Walgraeve C. Degradation of gaseous hydrocarbons in aerated stirred bioreactors inoculated with Rhodococcus erythropolis: Effect of the carbon source and SIFT-MS method development. J Environ Sci (China) 2025; 147:268-281. [PMID: 39003046 DOI: 10.1016/j.jes.2023.10.020] [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: 08/11/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 07/15/2024]
Abstract
The study of microbial hydrocarbons removal is of great importance for the development of future bioremediation strategies. In this study, we evaluated the removal of a gaseous mixture containing toluene, m-xylene, ethylbenzene, cyclohexane, butane, pentane, hexane and heptane in aerated stirred bioreactors inoculated with Rhodococcus erythropolis and operated under non-sterile conditions. For the real-time measurement of hydrocarbons, a novel systematic approach was implemented using Selected-Ion Flow Tube Mass Spectrometry (SIFT-MS). The effect of the carbon source (∼9.5 ppmv) on (i) the bioreactors' performance (BR1: dosed with only cyclohexane as a single hydrocarbon versus BR2: dosed with a mixture of the 8 hydrocarbons) and (ii) the evolution of microbial communities over time were investigated. The results showed that cyclohexane reached a maximum removal efficiency (RE) of 53% ± 4% in BR1. In BR2, almost complete removal of toluene, m-xylene and ethylbenzene, being the most water-soluble and easy-to-degrade carbon sources, was observed. REs below 32% were obtained for the remaining compounds. By exposing the microbial consortium to only the five most recalcitrant hydrocarbons, REs between 45% ± 5% and 98% ± 1% were reached. In addition, we observed that airborne microorganisms populated the bioreactors and that the type of carbon source influenced the microbial communities developed. The abundance of species belonging to the genus Rhodococcus was below 10% in all bioreactors at the end of the experiments. This work provides fundamental insights to understand the complex behavior of gaseous hydrocarbon mixtures in bioreactors, along with a systematic approach for the development of SIFT-MS methods.
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Affiliation(s)
- Paula Alejandra Lamprea Pineda
- Research group EnVOC, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent Belgium
| | - Kristof Demeestere
- Research group EnVOC, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent Belgium
| | - Allan Augusto Alvarado-Alvarado
- Research group EnVOC, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent Belgium
| | - Frank Devlieghere
- Research group FMFP, Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology - CMET, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent Belgium
| | - Herman Van Langenhove
- Research group EnVOC, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent Belgium
| | - Christophe Walgraeve
- Research group EnVOC, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent Belgium.
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23
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Hu Z, Yang J, Zhang S, Li M, Zuo C, Mao C, Zhang Z, Tang M, Shi C, Xu Y. AAV mediated carboxyl terminus of Hsp70 interacting protein overexpression mitigates the cognitive and pathological phenotypes of APP/PS1 mice. Neural Regen Res 2025; 20:253-264. [PMID: 38767490 PMCID: PMC11246129 DOI: 10.4103/nrr.nrr-d-23-01277] [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: 07/31/2023] [Revised: 11/27/2023] [Accepted: 01/02/2024] [Indexed: 05/22/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202501000-00033/figure1/v/2024-05-14T021156Z/r/image-tiff The E3 ubiquitin ligase, carboxyl terminus of heat shock protein 70 (Hsp70) interacting protein (CHIP), also functions as a co-chaperone and plays a crucial role in the protein quality control system. In this study, we aimed to investigate the neuroprotective effect of overexpressed CHIP on Alzheimer's disease. We used an adeno-associated virus vector that can cross the blood-brain barrier to mediate CHIP overexpression in APP/PS1 mouse brain. CHIP overexpression significantly ameliorated the performance of APP/PS1 mice in the Morris water maze and nest building tests, reduced amyloid-β plaques, and decreased the expression of both amyloid-β and phosphorylated tau. CHIP also alleviated the concentration of microglia and astrocytes around plaques. In APP/PS1 mice of a younger age, CHIP overexpression promoted an increase in ADAM10 expression and inhibited β-site APP cleaving enzyme 1, insulin degrading enzyme, and neprilysin expression. Levels of HSP70 and HSP40, which have functional relevance to CHIP, were also increased. Single nuclei transcriptome sequencing in the hippocampus of CHIP overexpressed mice showed that the lysosomal pathway and oligodendrocyte-related biological processes were up-regulated, which may also reflect a potential mechanism for the neuroprotective effect of CHIP. Our research shows that CHIP effectively reduces the behavior and pathological manifestations of APP/PS1 mice. Indeed, overexpression of CHIP could be a beneficial approach for the treatment of Alzheimer's disease.
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Affiliation(s)
- Zhengwei Hu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Academy of Medical Sciences of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Jing Yang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- NHC Key Laboratory of Prevention and treatment of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Shuo Zhang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Academy of Medical Sciences of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Mengjie Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Chunyan Zuo
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Chengyuan Mao
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- NHC Key Laboratory of Prevention and treatment of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Zhongxian Zhang
- Sino-British Research Centre for Molecular Oncology, National Centre for International Research in Cell and Gene Therapy, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Mibo Tang
- Department of Gerontology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Changhe Shi
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- NHC Key Laboratory of Prevention and treatment of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Yuming Xu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- NHC Key Laboratory of Prevention and treatment of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, Henan Province, China
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24
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Cong M, Hu JJ, Yu Y, Li XL, Sun XT, Wang LT, Wu X, Zhu LJ, Yang XJ, He QR, Ding F, Shi HY. miRNA-21-5p is an important contributor to the promotion of injured peripheral nerve regeneration using hypoxia-pretreated bone marrow-derived neural crest cells. Neural Regen Res 2025; 20:277-290. [PMID: 38767492 PMCID: PMC11246143 DOI: 10.4103/1673-5374.390956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 09/26/2023] [Indexed: 05/22/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202501000-00035/figure1/v/2024-05-14T021156Z/r/image-tiff Our previous study found that rat bone marrow-derived neural crest cells (acting as Schwann cell progenitors) have the potential to promote long-distance nerve repair. Cell-based therapy can enhance peripheral nerve repair and regeneration through paracrine bioactive factors and intercellular communication. Nevertheless, the complex contributions of various types of soluble cytokines and extracellular vesicle cargos to the secretome remain unclear. To investigate the role of the secretome and extracellular vesicles in repairing damaged peripheral nerves, we collected conditioned culture medium from hypoxia-pretreated neural crest cells, and found that it significantly promoted the repair of sensory neurons damaged by oxygen-glucose deprivation. The mRNA expression of trophic factors was highly expressed in hypoxia-pretreated neural crest cells. We performed RNA sequencing and bioinformatics analysis and found that miR-21-5p was enriched in hypoxia-pretreated extracellular vesicles of neural crest cells. Subsequently, to further clarify the role of hypoxia-pretreated neural crest cell extracellular vesicles rich in miR-21-5p in axonal growth and regeneration of sensory neurons, we used a microfluidic axonal dissociation model of sensory neurons in vitro, and found that hypoxia-pretreated neural crest cell extracellular vesicles promoted axonal growth and regeneration of sensory neurons, which was greatly dependent on loaded miR-21-5p. Finally, we constructed a miR-21-5p-loaded neural conduit to repair the sciatic nerve defect in rats and found that the motor and sensory functions of injured rat hind limb, as well as muscle tissue morphology of the hind limbs, were obviously restored. These findings suggest that hypoxia-pretreated neural crest extracellular vesicles are natural nanoparticles rich in miRNA-21-5p. miRNA-21-5p is one of the main contributors to promoting nerve regeneration by the neural crest cell secretome. This helps to explain the mechanism of action of the secretome and extracellular vesicles of neural crest cells in repairing damaged peripheral nerves, and also promotes the application of miR-21-5p in tissue engineering regeneration medicine.
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Affiliation(s)
- Meng Cong
- School of Medicine, Nantong University, Nantong, Jiangsu Province, China
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education and Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Jing-Jing Hu
- School of Medicine, Nantong University, Nantong, Jiangsu Province, China
- Department of Physiology, Jiangsu Health Vocational College, Nanjing, Jiangsu Province, China
| | - Yan Yu
- School of Medicine, Nantong University, Nantong, Jiangsu Province, China
| | - Xiao-Li Li
- School of Medicine, Nantong University, Nantong, Jiangsu Province, China
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Xiao-Ting Sun
- School of Medicine, Nantong University, Nantong, Jiangsu Province, China
| | - Li-Ting Wang
- School of Medicine, Nantong University, Nantong, Jiangsu Province, China
| | - Xia Wu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education and Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Ling-Jie Zhu
- School of Medicine, Nantong University, Nantong, Jiangsu Province, China
| | - Xiao-Jia Yang
- School of Medicine, Nantong University, Nantong, Jiangsu Province, China
| | - Qian-Ru He
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education and Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Fei Ding
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education and Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
- Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Hai-Yan Shi
- School of Medicine, Nantong University, Nantong, Jiangsu Province, China
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education and Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
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25
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Wang J, Yin J, Peng D, Zhang X, Shi Z, Li W, Shi Y, Sun M, Jiang N, Cheng B, Meng X, Liu R. 4-Nitrophenol at environmentally relevant concentrations mediates reproductive toxicity in Caenorhabditis elegans via metabolic disorders-induced estrogen signaling pathway. J Environ Sci (China) 2025; 147:244-258. [PMID: 39003044 DOI: 10.1016/j.jes.2023.09.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/16/2023] [Accepted: 09/24/2023] [Indexed: 07/15/2024]
Abstract
4-Nitrophenol (4-NP), as a toxic and refractory pollutant, has generated significant concern due to its adverse effects. However, the potential toxic effects and mechanism remained unclear. In this study, the reproduction, development, locomotion and reactive oxygen species (ROS) production of Caenorhabditis elegans were investigated to evaluate the 4-NP toxicity. We used metabolomics to assess the potential damage mechanisms. The role of metabolites in mediating the relationship between 4-NP and phenotypes was examined by correlation and mediation analysis. 4-NP (8 ng/L and 8 µg/L) caused significant reduction of brood size, ovulation rate, total germ cells numbers, head thrashes and body bends, and an increase in ROS. However, the oosperm numbers in uterus, body length and body width were decreased in 8 µg/L. Moreover, 36 differential metabolites were enriched in the significant metabolic pathways, including lysine biosynthesis, β-alanine metabolism, tryptophan metabolism, pentose phosphate pathway, pentose and glucuronate interconversions, amino sugar and nucleotide sugar metabolism, starch and sucrose metabolism, galactose metabolism, propanoate metabolism, glycerolipid metabolism, and estrogen signaling pathway. The mechanism of 4-NP toxicity was that oxidative stress caused by the perturbation of amino acid, which had effects on energy metabolism through disturbing carbohydrate and lipid metabolism, and finally affected the estrogen signaling pathway to exert toxic effects. Moreover, correlation and mediation analysis showed glycerol-3P, glucosamine-6P, glucosamine-1P, UDP-galactose, L-aspartic acid, and uracil were potential markers for the reproduction and glucose-1,6P2 for developmental toxicity. The results provided insight into the pathways involved in the toxic effects caused by 4-NP and developed potential biomarkers to evaluate 4-NP toxicity.
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Affiliation(s)
- Jia Wang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Jiechen Yin
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Danhong Peng
- Department of Obstetrics and Gynecology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China
| | - Xiaoqian Zhang
- Department of Obstetrics and Gynecology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215002, China
| | - Zhouhong Shi
- Department of Obstetrics and Gynecology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215002, China
| | - Weixi Li
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Yingchi Shi
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Mingjun Sun
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Nan Jiang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Beijing Cheng
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Xingchen Meng
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Ran Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
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Wang Y, Ning X, Liang J, Wang A, Qu J. Enhancing microbial superoxide generation and conversion to hydroxyl radicals for enhanced bioremediation using iron-binding ligands. J Environ Sci (China) 2025; 147:597-606. [PMID: 39003074 DOI: 10.1016/j.jes.2023.11.023] [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: 09/09/2023] [Revised: 11/22/2023] [Accepted: 11/22/2023] [Indexed: 07/15/2024]
Abstract
Harnessing bacteria for superoxide production in bioremediation holds immense promise, yet its practical application is hindered by slow production rates and the relatively weak redox potential of superoxide. This study delves into a cost-effective approach to amplify superoxide production using an Arthrobacter strain, a prevalent soil bacterial genus. Our research reveals that introducing a carbon source along with specific iron-binding ligands, including deferoxamine (DFO), diethylenetriamine pentaacetate (DTPA), citrate, and oxalate, robustly augments microbial superoxide generation. Moreover, our findings suggest that these iron-binding ligands play a pivotal role in converting superoxide into hydroxyl radicals by modulating the electron transfer rate between Fe(III)/Fe(II) and superoxide. Remarkably, among the tested ligands, only DTPA emerges as a potent promoter of this conversion process when complexed with Fe(III). We identify an optimal Fe(III) to DTPA ratio of approximately 1:1 for enhancing hydroxyl radical production within the Arthrobacter culture. This research underscores the efficacy of simultaneously introducing carbon sources and DTPA in facilitating superoxide production and its subsequent conversion to hydroxyl radicals, significantly elevating bioremediation performance. Furthermore, our study reveals that DTPA augments superoxide production in cultures of diverse soils, with various soil microorganisms beyond Arthrobacter identified as contributors to superoxide generation. This emphasizes the universal applicability of DTPA across multiple bacterial genera. In conclusion, our study introduces a promising methodology for enhancing microbial superoxide production and its conversion into hydroxyl radicals. These findings hold substantial implications for the deployment of microbial reactive oxygen species in bioremediation, offering innovative solutions for addressing environmental contamination challenges.
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Affiliation(s)
- Yuhan Wang
- School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Xue Ning
- SFI MaREI Centre for Energy, Climate and Marine, Environmental Research Institute, University College Cork, Cork, Ireland
| | - Jinsong Liang
- School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China.
| | - Aijie Wang
- School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Jiuhui Qu
- Center for Water and Ecology, Tsinghua University, Beijing 100084, China
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27
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Hu D, Cao Y, Cai C, Wang G, Zhou M, Peng L, Fan Y, Lai Q, Gao Z. Establishment of human cerebral organoid systems to model early neural development and assess the central neurotoxicity of environmental toxins. Neural Regen Res 2025; 20:242-252. [PMID: 38767489 PMCID: PMC11246146 DOI: 10.4103/nrr.nrr-d-23-00928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 12/08/2023] [Indexed: 05/22/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202501000-00032/figure1/v/2024-05-14T021156Z/r/image-tiff Human brain development is a complex process, and animal models often have significant limitations. To address this, researchers have developed pluripotent stem cell-derived three-dimensional structures, known as brain-like organoids, to more accurately model early human brain development and disease. To enable more consistent and intuitive reproduction of early brain development, in this study, we incorporated forebrain organoid culture technology into the traditional unguided method of brain organoid culture. This involved embedding organoids in matrigel for only 7 days during the rapid expansion phase of the neural epithelium and then removing them from the matrigel for further cultivation, resulting in a new type of human brain organoid system. This cerebral organoid system replicated the temporospatial characteristics of early human brain development, including neuroepithelium derivation, neural progenitor cell production and maintenance, neuron differentiation and migration, and cortical layer patterning and formation, providing more consistent and reproducible organoids for developmental modeling and toxicology testing. As a proof of concept, we applied the heavy metal cadmium to this newly improved organoid system to test whether it could be used to evaluate the neurotoxicity of environmental toxins. Brain organoids exposed to cadmium for 7 or 14 days manifested severe damage and abnormalities in their neurodevelopmental patterns, including bursts of cortical cell death and premature differentiation. Cadmium exposure caused progressive depletion of neural progenitor cells and loss of organoid integrity, accompanied by compensatory cell proliferation at ectopic locations. The convenience, flexibility, and controllability of this newly developed organoid platform make it a powerful and affordable alternative to animal models for use in neurodevelopmental, neurological, and neurotoxicological studies.
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Affiliation(s)
- Daiyu Hu
- Fundamental Research Center, Shanghai Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), School of Medicine, Tongji University, Shanghai, China
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), Shanghai University School of Medicine, Nantong, Jiangsu Province, China
- Shanghai Engineering Research Center of Organ Repair, Shanghai University School of Medicine, Shanghai, China
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yuanqing Cao
- Fundamental Research Center, Shanghai Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), School of Medicine, Tongji University, Shanghai, China
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), Shanghai University School of Medicine, Nantong, Jiangsu Province, China
- Shanghai Engineering Research Center of Organ Repair, Shanghai University School of Medicine, Shanghai, China
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Chenglin Cai
- Fundamental Research Center, Shanghai Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), School of Medicine, Tongji University, Shanghai, China
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Guangming Wang
- Fundamental Research Center, Shanghai Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), School of Medicine, Tongji University, Shanghai, China
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Min Zhou
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), Shanghai University School of Medicine, Nantong, Jiangsu Province, China
- Shanghai Engineering Research Center of Organ Repair, Shanghai University School of Medicine, Shanghai, China
| | - Luying Peng
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yantao Fan
- Fundamental Research Center, Shanghai Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), School of Medicine, Tongji University, Shanghai, China
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), Shanghai University School of Medicine, Nantong, Jiangsu Province, China
- Shanghai Engineering Research Center of Organ Repair, Shanghai University School of Medicine, Shanghai, China
| | - Qiong Lai
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), Shanghai University School of Medicine, Nantong, Jiangsu Province, China
- Shanghai Engineering Research Center of Organ Repair, Shanghai University School of Medicine, Shanghai, China
| | - Zhengliang Gao
- Fundamental Research Center, Shanghai Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), School of Medicine, Tongji University, Shanghai, China
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), Shanghai University School of Medicine, Nantong, Jiangsu Province, China
- Shanghai Engineering Research Center of Organ Repair, Shanghai University School of Medicine, Shanghai, China
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28
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Yuan Y, Yu L, Zhuang X, Wen D, He J, Hong J, Xie J, Ling S, Du X, Chen W, Wang X. Drosophila models used to simulate human ATP1A1 gene mutations that cause Charcot-Marie-Tooth type 2 disease and refractory seizures. Neural Regen Res 2025; 20:265-276. [PMID: 38767491 PMCID: PMC11246156 DOI: 10.4103/1673-5374.391302] [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: 04/25/2023] [Revised: 09/21/2023] [Accepted: 11/06/2023] [Indexed: 05/22/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202501000-00034/figure1/v/2024-05-14T021156Z/r/image-tiff Certain amino acids changes in the human Na+/K+-ATPase pump, ATPase Na+/K+ transporting subunit alpha 1 (ATP1A1), cause Charcot-Marie-Tooth disease type 2 (CMT2) disease and refractory seizures. To develop in vivo models to study the role of Na+/K+-ATPase in these diseases, we modified the Drosophila gene homolog, Atpα, to mimic the human ATP1A1 gene mutations that cause CMT2. Mutations located within the helical linker region of human ATP1A1 (I592T, A597T, P600T, and D601F) were simultaneously introduced into endogenous DrosophilaAtpα by CRISPR/Cas9-mediated genome editing, generating the AtpαTTTF model. In addition, the same strategy was used to generate the corresponding single point mutations in flies (AtpαI571T, AtpαA576T, AtpαP579T, and AtpαD580F). Moreover, a deletion mutation (Atpαmut) that causes premature termination of translation was generated as a positive control. Of these alleles, we found two that could be maintained as homozygotes (AtpαI571T and AtpαP579T). Three alleles (AtpαA576T, AtpαP579 and AtpαD580F) can form heterozygotes with the Atpαmut allele. We found that the Atpα allele carrying these CMT2-associated mutations showed differential phenotypes in Drosophila. Flies heterozygous for AtpαTTTF mutations have motor performance defects, a reduced lifespan, seizures, and an abnormal neuronal morphology. These Drosophila models will provide a new platform for studying the function and regulation of the sodium-potassium pump.
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Affiliation(s)
- Yao Yuan
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian Province, China
| | - Lingqi Yu
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian Province, China
| | - Xudong Zhuang
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate (Fujian Maternity and Child Health Hospital), Fuzhou, Fujian Province, China
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Dongjing Wen
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian Province, China
| | - Jin He
- Department of Neurology and Institute of Neurology of The First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Jingmei Hong
- Department of Neurology and Institute of Neurology of The First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Jiayu Xie
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian Province, China
| | - Shengan Ling
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian Province, China
| | - Xiaoyue Du
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian Province, China
| | - Wenfeng Chen
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian Province, China
| | - Xinrui Wang
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate (Fujian Maternity and Child Health Hospital), Fuzhou, Fujian Province, China
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian Province, China
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Sun SY, Nie L, Zhang J, Fang X, Luo H, Fu C, Wei Z, Tang AH. The interaction between KIF21A and KANK1 regulates dendritic morphology and synapse plasticity in neurons. Neural Regen Res 2025; 20:209-223. [PMID: 38767486 PMCID: PMC11246154 DOI: 10.4103/1673-5374.391301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 11/07/2023] [Indexed: 05/22/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202501000-00029/figure1/v/2024-05-14T021156Z/r/image-tiff Morphological alterations in dendritic spines have been linked to changes in functional communication between neurons that affect learning and memory. Kinesin-4 KIF21A helps organize the microtubule-actin network at the cell cortex by interacting with KANK1; however, whether KIF21A modulates dendritic structure and function in neurons remains unknown. In this study, we found that KIF21A was distributed in a subset of dendritic spines, and that these KIF21A-positive spines were larger and more structurally plastic than KIF21A-negative spines. Furthermore, the interaction between KIF21A and KANK1 was found to be critical for dendritic spine morphogenesis and synaptic plasticity. Knockdown of either KIF21A or KANK1 inhibited dendritic spine morphogenesis and dendritic branching, and these deficits were fully rescued by coexpressing full-length KIF21A or KANK1, but not by proteins with mutations disrupting direct binding between KIF21A and KANK1 or binding between KANK1 and talin1. Knocking down KIF21A in the hippocampus of rats inhibited the amplitudes of long-term potentiation induced by high-frequency stimulation and negatively impacted the animals' cognitive abilities. Taken together, our findings demonstrate the function of KIF21A in modulating spine morphology and provide insight into its role in synaptic function.
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Affiliation(s)
- Shi-Yan Sun
- Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, Ministry of Education Key Laboratory for Membrane-less Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui Province, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, Anhui Province, China
| | - Lingyun Nie
- Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, Ministry of Education Key Laboratory for Membrane-less Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui Province, China
- CAS Center for Excellence in Molecular Cell Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui Province, China
| | - Jing Zhang
- Department of Neurobiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
- Brain Research Center, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Xue Fang
- Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, Ministry of Education Key Laboratory for Membrane-less Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui Province, China
| | - Hongmei Luo
- Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, Ministry of Education Key Laboratory for Membrane-less Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui Province, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, Anhui Province, China
| | - Chuanhai Fu
- Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, Ministry of Education Key Laboratory for Membrane-less Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui Province, China
- CAS Center for Excellence in Molecular Cell Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui Province, China
| | - Zhiyi Wei
- Department of Neurobiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
- Brain Research Center, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Ai-Hui Tang
- Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, Ministry of Education Key Laboratory for Membrane-less Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui Province, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, Anhui Province, China
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30
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Lan C, Fang G, Qiu C, Li X, Yang F, Yang Y. Inhibition of DYRK1A attenuates vascular remodeling in pulmonary arterial hypertension via suppressing STAT3/Pim-1/NFAT pathway. Clin Exp Hypertens 2024; 46:2297642. [PMID: 38147409 DOI: 10.1080/10641963.2023.2297642] [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: 08/24/2023] [Accepted: 12/15/2023] [Indexed: 12/28/2023]
Abstract
Pulmonary arterial hypertension (PAH) is characterized by progressive vascular remodeling caused by the excessive proliferation and survival of pulmonary artery smooth muscle cells (PASMCs). Dual-specificity tyrosine regulated kinase 1A (DYRK1A) is a pleiotropic kinase involved in the regulation of multiple biological functions, including cell proliferation and survival. However, the role and underlying mechanisms of DYRK1A in PAH pathogenesis remain unclear. We found that DYRK1A was upregulated in PASMCs in response to hypoxia, both in vivo and in vitro. Inhibition of DYRK1A by harmine significantly attenuated hypoxia-induced pulmonary hypertension and pulmonary artery remodeling. Mechanistically, we found that DYRK1A promoted pulmonary arterial remodeling by enhancing the proliferation and survival of PASMCs through activating the STAT3/Pim-1/NFAT pathway, because STAT3 gain-of-function via adeno-associated virus serotype 2 (AAV2) carrying the constitutively active form of STAT3 (STAT3C) nearly abolished the protective effect of harmine on PAH. Collectively, our results reveal a significant role for DYRK1A in pulmonary arterial remodeling and suggest it as a drug target with translational potential for the treatment of PAH.
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Affiliation(s)
- Cong Lan
- Department of Cardiology, General Hospital of Western Theater Command, Chengdu, Sichuan, China
| | - Guangyao Fang
- Department of Cardiology, General Hospital of Western Theater Command, Chengdu, Sichuan, China
| | - Chenming Qiu
- Department of Burn and Plastic Surgery, General Hospital of Western Theater Command, Chengdu, Sichuan, China
| | - Xiuchuan Li
- Department of Cardiology, General Hospital of Western Theater Command, Chengdu, Sichuan, China
| | - Fengyuan Yang
- Department of Nephrology, General Hospital of Western Theater Command, Chengdu, Sichuan, China
| | - Yongjian Yang
- Department of Cardiology, General Hospital of Western Theater Command, Chengdu, Sichuan, China
- College of Medicine, Southwest Jiaotong University, Chengdu, Sichuan, China
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31
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Sehgal M, Nayak SP, Sahoo S, Somarelli JA, Jolly MK. Mutually exclusive teams-like patterns of gene regulation characterize phenotypic heterogeneity along the noradrenergic-mesenchymal axis in neuroblastoma. Cancer Biol Ther 2024; 25:2301802. [PMID: 38230570 PMCID: PMC10795782 DOI: 10.1080/15384047.2024.2301802] [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: 09/08/2023] [Accepted: 01/01/2024] [Indexed: 01/18/2024] Open
Abstract
Neuroblastoma is the most frequent extracranial pediatric tumor and leads to 15% of all cancer-related deaths in children. Tumor relapse and therapy resistance in neuroblastoma are driven by phenotypic plasticity and heterogeneity between noradrenergic (NOR) and mesenchymal (MES) cell states. Despite the importance of this phenotypic plasticity, the dynamics and molecular patterns associated with these bidirectional cell-state transitions remain relatively poorly understood. Here, we analyze multiple RNA-seq datasets at both bulk and single-cell resolution, to understand the association between NOR- and MES-specific factors. We observed that NOR-specific and MES-specific expression patterns are largely mutually exclusive, exhibiting a "teams-like" behavior among the genes involved, reminiscent of our earlier observations in lung cancer and melanoma. This antagonism between NOR and MES phenotypes was also associated with metabolic reprogramming and with immunotherapy targets PD-L1 and GD2 as well as with experimental perturbations driving the NOR-MES and/or MES-NOR transition. Further, these "teams-like" patterns were seen only among the NOR- and MES-specific genes, but not in housekeeping genes, possibly highlighting a hallmark of network topology enabling cancer cell plasticity.
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Affiliation(s)
- Manas Sehgal
- Department of Bioengineering, Indian Institute of Science, Bangalore, India
| | - Sonali Priyadarshini Nayak
- Department of Bioengineering, Indian Institute of Science, Bangalore, India
- Max Planck School Matter to Life, University of Göttingen, Göttingen, Germany
| | - Sarthak Sahoo
- Department of Bioengineering, Indian Institute of Science, Bangalore, India
| | | | - Mohit Kumar Jolly
- Department of Bioengineering, Indian Institute of Science, Bangalore, India
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32
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Wang Q, Su Z, Zhang J, Yan H, Zhang J. Unraveling the copper-death connection: Decoding COVID-19's immune landscape through advanced bioinformatics and machine learning approaches. Hum Vaccin Immunother 2024; 20:2310359. [PMID: 38468184 PMCID: PMC10936617 DOI: 10.1080/21645515.2024.2310359] [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: 09/01/2023] [Accepted: 01/23/2024] [Indexed: 03/13/2024] Open
Abstract
This study aims to analyze Coronavirus Disease 2019 (COVID-19)-associated copper-death genes using the Gene Expression Omnibus (GEO) dataset and machine learning, exploring their immune microenvironment correlation and underlying mechanisms. Utilizing GEO, we analyzed the GSE217948 dataset with control samples. Differential expression analysis identified 16 differentially expressed copper-death genes, and Cell type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) quantified immune cell infiltration. Gene classification yielded two copper-death clusters, with Weighted Gene Co-expression Network Analysis (WGCNA) identifying key module genes. Machine learning models (random forest, Support Vector Machine (SVM), Generalized Linear Model (GLM), eXtreme Gradient Boosting (XGBoost)) selected 6 feature genes validated by the GSE213313 dataset. Ferredoxin 1 (FDX1) emerged as the top gene, corroborated by Area Under the Curve (AUC) analysis. Gene Set Enrichment Analysis (GSEA) and Gene Set Variation Analysis (GSVA) revealed enriched pathways in T cell receptor, natural killer cytotoxicity, and Peroxisome Proliferator-Activated Receptor (PPAR). We uncovered differentially expressed copper-death genes and immune infiltration differences, notably CD8 T cells and M0 macrophages. Clustering identified modules with potential implications for COVID-19. Machine learning models effectively predicted COVID-19 risk, with FDX1's pivotal role validated. FDX1's high expression was associated with immune pathways, suggesting its role in COVID-19 pathogenesis. This comprehensive approach elucidated COVID-19-related copper-death genes, their immune context, and risk prediction potential. FDX1's connection to immune pathways offers insights into COVID-19 mechanisms and therapy.
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Affiliation(s)
- Qi Wang
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Zhenzhong Su
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Jing Zhang
- Department of General Gynecology, The First Hospital of Jilin University, Changchun, Jilin, China
| | - He Yan
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Jie Zhang
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Jilin University, Changchun, Jilin, China
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33
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Chen Z, Xie H, Liu J, Zhao J, Huang R, Xiang Y, Wu H, Tian D, Bian E, Xiong Z. Roles of TRPM channels in glioma. Cancer Biol Ther 2024; 25:2338955. [PMID: 38680092 PMCID: PMC11062369 DOI: 10.1080/15384047.2024.2338955] [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: 12/03/2023] [Accepted: 04/01/2024] [Indexed: 05/01/2024] Open
Abstract
Gliomas are the most common type of primary brain tumor. Despite advances in treatment, it remains one of the most aggressive and deadly tumor of the central nervous system (CNS). Gliomas are characterized by high malignancy, heterogeneity, invasiveness, and high resistance to radiotherapy and chemotherapy. It is urgent to find potential new molecular targets for glioma. The TRPM channels consist of TRPM1-TPRM8 and play a role in many cellular functions, including proliferation, migration, invasion, angiogenesis, etc. More and more studies have shown that TRPM channels can be used as new therapeutic targets for glioma. In this review, we first introduce the structure, activation patterns, and physiological functions of TRPM channels. Additionally, the pathological mechanism of glioma mediated by TRPM2, 3, 7, and 8 and the related signaling pathways are described. Finally, we discuss the therapeutic potential of targeting TRPM for glioma.
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Affiliation(s)
- Zhigang Chen
- Department of Neurosurgery, The Translational Research Institute for Neurological Disorders, The First Affiliated Hospital (Yijishan Hospital), Wannan Medical College, Wuhu, P. R. China
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, China
| | - Han Xie
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, China
| | - Jun Liu
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - JiaJia Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, China
| | - Ruixiang Huang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, China
| | - Yufei Xiang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, China
| | - Haoyuan Wu
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, China
| | - Dasheng Tian
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Erbao Bian
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhang Xiong
- Department of Neurosurgery, The Translational Research Institute for Neurological Disorders, The First Affiliated Hospital (Yijishan Hospital), Wannan Medical College, Wuhu, P. R. China
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Ramirez M, Bastien E, Chae H, Gianello P, Gilon P, Bouzin C. 3D evaluation of the extracellular matrix of hypoxic pancreatic islets using light sheet fluorescence microscopy. Islets 2024; 16:2298518. [PMID: 38267218 PMCID: PMC10810165 DOI: 10.1080/19382014.2023.2298518] [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: 08/02/2023] [Accepted: 12/19/2023] [Indexed: 01/26/2024] Open
Abstract
Pancreatic islet transplantation is a promising treatment for type 1 diabetes, but the survival and function of transplanted islets are hindered by the loss of extracellular matrix (ECM) during islet isolation and by low oxygenation upon implantation. This study aimed to evaluate the impact of hypoxia on ECM using a cutting-edge imaging approach based on tissue clearing and 3D microscopy. Human and rat islets were cultured under normoxic (O2 21%) or hypoxic (O2 1%) conditions. Immunofluorescence staining targeting insulin, glucagon, CA9 (a hypoxia marker), ECM proteins (collagen 4, fibronectin, laminin), and E-cadherin (intercellular adhesion protein) was performed on fixed whole islets. The cleared islets were imaged using Light Sheet Fluorescence Microscopy (LSFM) and digitally analyzed. The volumetric analysis of target proteins did not show significant differences in abundance between the experimental groups. However, 3D projections revealed distinct morphological features that differentiated normoxic and hypoxic islets. Under normoxic conditions, ECM could be found throughout the islets. Hypoxic islets exhibited areas of scattered nuclei and central clusters of ECM proteins, indicating central necrosis. E-cadherin was absent in these areas. Our results, demonstrating a diminution of islets' functional mass in hypoxia, align with the functional decline observed in transplanted islets experiencing low oxygenation after grafting. This study provides a methodology combining tissue clearing, multiplex immunofluorescence, Light Sheet Fluorescence Microscopy, and digital image analysis to investigate pancreatic islet morphology. This 3D approach allowed us to highlight ECM organizational changes during hypoxia from a morphological perspective.
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Affiliation(s)
- Matias Ramirez
- Pole of Experimental Surgery and Transplantation, Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium
| | - Estelle Bastien
- Pole of Pharmacology and Therapeutics, Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium
| | - Heeyoung Chae
- Pole of Endocrinology, Diabetes and Nutrition, Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium
| | - Pierre Gianello
- Laboratory of Experimental Surgery and Transplantation, Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium
| | - Patrick Gilon
- Pole of Endocrinology, Diabetes and Nutrition, Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium
| | - Caroline Bouzin
- Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Brussels, Belgium
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Parves MR, Solares MJ, Dearnaley WJ, Kelly DF. Elucidating structural variability in p53 conformers using combinatorial refinement strategies and molecular dynamics. Cancer Biol Ther 2024; 25:2290732. [PMID: 38073067 PMCID: PMC10732606 DOI: 10.1080/15384047.2023.2290732] [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: 09/12/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Low molecular weight proteins and protein assemblies can now be investigated using cryo-electron microscopy (EM) as a complement to traditional structural biology techniques. It is important, however, to not lose sight of the dynamic information inherent in macromolecules that give rise to their exquisite functionality. As computational methods continue to advance the field of biomedical imaging, so must strategies to resolve the minute details of disease-related entities. Here, we employed combinatorial modeling approaches to assess flexible properties among low molecular weight proteins (~100 kDa or less). Through a blend of rigid body refinement and simulated annealing, we determined new hidden conformations for wild type p53 monomer and dimer forms. Structures for both states converged to yield new conformers, each revealing good stereochemistry and dynamic information about the protein. Based on these insights, we identified fluid parts of p53 that complement the stable central core of the protein responsible for engaging DNA. Molecular dynamics simulations corroborated the modeling results and helped pinpoint the more flexible residues in wild type p53. Overall, the new computational methods may be used to shed light on other small protein features in a vast ensemble of structural data that cannot be easily delineated by other algorithms.
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Affiliation(s)
- Md Rimon Parves
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
- Biochemistry, Microbiology, and Molecular Biology Graduate Program, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Maria J. Solares
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
- Molecular, Cellular, and Integrative Biosciences Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - William J. Dearnaley
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
| | - Deborah F. Kelly
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
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Aparicio B, Theunissen P, Hervas-Stubbs S, Fortes P, Sarobe P. Relevance of mutation-derived neoantigens and non-classical antigens for anticancer therapies. Hum Vaccin Immunother 2024; 20:2303799. [PMID: 38346926 PMCID: PMC10863374 DOI: 10.1080/21645515.2024.2303799] [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: 09/29/2023] [Accepted: 01/06/2024] [Indexed: 02/15/2024] Open
Abstract
Efficacy of cancer immunotherapies relies on correct recognition of tumor antigens by lymphocytes, eliciting thus functional responses capable of eliminating tumor cells. Therefore, important efforts have been carried out in antigen identification, with the aim of understanding mechanisms of response to immunotherapy and to design safer and more efficient strategies. In addition to classical tumor-associated antigens identified during the last decades, implementation of next-generation sequencing methodologies is enabling the identification of neoantigens (neoAgs) arising from mutations, leading to the development of new neoAg-directed therapies. Moreover, there are numerous non-classical tumor antigens originated from other sources and identified by new methodologies. Here, we review the relevance of neoAgs in different immunotherapies and the results obtained by applying neoAg-based strategies. In addition, the different types of non-classical tumor antigens and the best approaches for their identification are described. This will help to increase the spectrum of targetable molecules useful in cancer immunotherapies.
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Affiliation(s)
- Belen Aparicio
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
| | - Patrick Theunissen
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
- DNA and RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Sandra Hervas-Stubbs
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
| | - Puri Fortes
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
- DNA and RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Spanish Network for Advanced Therapies (TERAV ISCIII), Spain
| | - Pablo Sarobe
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
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37
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Ren J, Zhao S, Lai J. Role and mechanism of COL3A1 in regulating the growth, metastasis, and drug sensitivity in cisplatin-resistant non-small cell lung cancer cells. Cancer Biol Ther 2024; 25:2328382. [PMID: 38530094 DOI: 10.1080/15384047.2024.2328382] [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: 12/05/2023] [Accepted: 03/05/2024] [Indexed: 03/27/2024] Open
Abstract
Non-small cell lung cancer (NSCLC) is among the most difficult malignancies to treat. Type III collagen (COL3A1) can affect the progression and chemoresistance development of NSCLC. We herein explored the mechanism that drives COL3A1 dysregulation in NSCLC. Potential RNA-binding proteins (RBPs) and transcription factors (TFs) that could bind to COL3A1 were searched by bioinformatics. mRNA expression was detected by quantitative PCR. Protein expression was evaluated using immunoblotting and immunohistochemistry. The effects of the variables were assessed by gauging cell growth, invasiveness, migratory capacity, apoptosis, and cisplatin (DDP) sensitivity. The direct YY1/COL3A1 relationship was confirmed by ChIP and luciferase reporter experiments. Xenograft experiments were done to examine COL3A1's function in DDP efficacy. COL3A1 showed enhanced expression in DDP-resistant NSCLC. In H460/DDP and A549/DDP cells, downregulation of COL3A1 exerted inhibitory functions in cell growth, invasiveness, and migration, as well as promoting effects on cell DDP sensitivity and apoptosis. Mechanistically, ELAV-like RNA binding protein 1 (ELAVL1) enhanced the mRNA stability and expression of COL3A1, and Yin Yang 1 (YY1) promoted the transcription and expression of COL3A1. Furthermore, upregulation of COL3A1 reversed ELAVL1 inhibition- or YY1 deficiency-mediated functions in DDP-resistant NSCLC cells. Additionally, COL3A1 downregulation enhanced the anti-tumor efficacy of DDP in vivo. Our investigation demonstrates that COL3A1 upregulation, induced by both RBP ELAVL1 and TF YY1, exerts important functions in phenotypes of NSCLC cells with DDP resistance, offering an innovative opportunity in the treatment of drug-resistant NSCLC.
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Affiliation(s)
- Jiankun Ren
- Nursing School, Hebi Polytechnic, Hebi City, China
| | - Songwei Zhao
- Nursing School, Hebi Polytechnic, Hebi City, China
| | - Junyu Lai
- Department of Cardiology, Affiliated Hospital of Jiangxi University of Chinese Medicine, Nanchang, Jiangxi, China
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Bahk S, Ahsan N, An J, Kim SH, Ramadany Z, Hong JC, Thelen JJ, Chung WS. Identification of mitogen-activated protein kinases substrates in Arabidopsis using kinase client assay. PLANT SIGNALING & BEHAVIOR 2024; 19:2326238. [PMID: 38493505 PMCID: PMC10950278 DOI: 10.1080/15592324.2024.2326238] [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: 11/24/2023] [Accepted: 02/25/2024] [Indexed: 03/19/2024]
Abstract
Mitogen-activated protein kinase (MPK) cascades are essential signal transduction components that control a variety of cellular responses in all eukaryotes. MPKs convert extracellular stimuli into cellular responses by the phosphorylation of downstream substrates. Although MPK cascades are predicted to be very complex, only limited numbers of MPK substrates have been identified in plants. Here, we used the kinase client (KiC) assay to identify novel substrates of MPK3 and MPK6. Recombinant MPK3 or MPK6 were tested against a large synthetic peptide library representing in vivo phosphorylation sites, and phosphorylated peptides were identified by high-resolution tandem mass spectrometry. From this screen, we identified 23 and 21 putative client peptides of MPK3 and MPK6, respectively. To verify the phosphorylation of putative client peptides, we performed in vitro kinase assay with recombinant fusion proteins of isolated client peptides. We found that 13 and 9 recombinant proteins were phosphorylated by MPK3 and MPK6. Among them, 11 proteins were proven to be the novel substrates of two MPKs. This study suggests that the KiC assay is a useful method to identify new substrates of MPKs.
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Affiliation(s)
- Sunghwa Bahk
- Division of Applied Life Science (BK21 Four program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Nagib Ahsan
- Department of Biochemistry and Interdisciplinary Plant Group, Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
- Mass Spectrometry, Proteomics and Metabolomics Core Facility, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK, USA
| | - Jonguk An
- Division of Applied Life Science (BK21 Four program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Sun Ho Kim
- Division of Applied Life Science (BK21 Four program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Zakiyah Ramadany
- Division of Applied Life Science (BK21 Four program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Jong Chan Hong
- Division of Applied Life Science (BK21 Four program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Jay J. Thelen
- Department of Biochemistry and Interdisciplinary Plant Group, Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Woo Sik Chung
- Division of Applied Life Science (BK21 Four program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
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Dian Y, Liu Y, Zeng F, Sun Y, Deng G. Efficacy and safety of tebentafusp in patients with metastatic uveal melanoma: A systematic review and meta-analysis. Hum Vaccin Immunother 2024; 20:2374647. [PMID: 39004419 PMCID: PMC11249029 DOI: 10.1080/21645515.2024.2374647] [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: 04/23/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024] Open
Abstract
Patients with metastatic uveal melanoma (mUM) have a poor prognosis, and few appropriate medications are available. Tebentafusp is approved by the Food and Drug Administration for mUM recently. However, the real efficacy and safety of tebentafusp are still unclear. We searched PubMed, Embase, and Cochrane Library from inception to March 20, 2024. The research was reported based on the preferred reporting items for systematic reviews and meta-analysis guidelines. We used random effects models to aggregate data on the response rates and adverse events of tebentafusp therapy. Six studies met the inclusion criteria with a total sample of 589 participants. The pooled objective response rate was 0.08 (95% CI: 0.05-0.12), and pooled disease control rate was 0.51 (95% CI: 0.44-0.57). The overall incidence was 0.99 (95% CI: 0.95-1.00) for any grade adverse events, 0.50 (95% CI: 0.41-0.59) for grade 3-4 adverse events, and 0.01 (95% CI: 0-0.03) for discontinuation due to adverse events. Tebentafusp exhibits promising treatment outcomes for mUM patients. Although accompanied with a common occurrence of adverse events, which can typically be managed and controlled. Future research is necessary for substantiating these findings and refining guidelines for management of mUM.
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Affiliation(s)
- Yating Dian
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, China
- Hunan Engineering Research Center of Skin Health and Disease, Central South University, Changsha, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Central South University, Changsha, China
- National Clinical Research Center of Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yihuang Liu
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, China
- Hunan Engineering Research Center of Skin Health and Disease, Central South University, Changsha, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Central South University, Changsha, China
- National Clinical Research Center of Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Furong Zeng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yuming Sun
- Department of Plastic and Cosmetic Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Guangtong Deng
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, China
- Hunan Engineering Research Center of Skin Health and Disease, Central South University, Changsha, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Central South University, Changsha, China
- National Clinical Research Center of Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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Sanjuan-Badillo A, P. Martínez-Castilla L, García-Sandoval R, Ballester P, Ferrándiz C, Sanchez MDLP, García-Ponce B, Garay-Arroyo A, R. Álvarez-Buylla E. HDACs MADS-domain protein interaction: a case study of HDA15 and XAL1 in Arabidopsis thaliana. PLANT SIGNALING & BEHAVIOR 2024; 19:2353536. [PMID: 38771929 PMCID: PMC11110687 DOI: 10.1080/15592324.2024.2353536] [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: 02/27/2024] [Accepted: 05/01/2024] [Indexed: 05/23/2024]
Abstract
Cellular behavior, cell differentiation and ontogenetic development in eukaryotes result from complex interactions between epigenetic and classic molecular genetic mechanisms, with many of these interactions still to be elucidated. Histone deacetylase enzymes (HDACs) promote the interaction of histones with DNA by compacting the nucleosome, thus causing transcriptional repression. MADS-domain transcription factors are highly conserved in eukaryotes and participate in controlling diverse developmental processes in animals and plants, as well as regulating stress responses in plants. In this work, we focused on finding out putative interactions of Arabidopsis thaliana HDACs and MADS-domain proteins using an evolutionary perspective combined with bioinformatics analyses and testing the more promising predicted interactions through classic molecular biology tools. Through bioinformatic analyses, we found similarities between HDACs proteins from different organisms, which allowed us to predict a putative protein-protein interaction between the Arabidopsis thaliana deacetylase HDA15 and the MADS-domain protein XAANTAL1 (XAL1). The results of two-hybrid and Bimolecular Fluorescence Complementation analysis demonstrated in vitro and in vivo HDA15-XAL1 interaction in the nucleus. Likely, this interaction might regulate developmental processes in plants as is the case for this type of interaction in animals.
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Affiliation(s)
- Andrea Sanjuan-Badillo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Programa de Doctorado en Ciencias Biomédicas, de la Universidad Nacional Autónoma de México, Ciudad de México, México
| | - León P. Martínez-Castilla
- Investigadoras e Investigadores por México, Grupo de Genómica y Dinámica Evolutiva de Microorganismos Emergentes, Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
| | | | - Patricia Ballester
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV Universidad Politécnica de Valencia, Valencia, España
| | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV Universidad Politécnica de Valencia, Valencia, España
| | - Maria de la Paz Sanchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
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Huynh DT, Nolfi E, Medfai L, van Ulsen P, Jong WSP, Sijts AJAM, Luirink J. Intranasal delivery of Salmonella OMVs decorated with Chlamydia trachomatis antigens induces specific local and systemic immune responses. Hum Vaccin Immunother 2024; 20:2330768. [PMID: 38517203 PMCID: PMC10962599 DOI: 10.1080/21645515.2024.2330768] [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: 08/03/2023] [Accepted: 03/12/2024] [Indexed: 03/23/2024] Open
Abstract
Chlamydia trachomatis is an obligate intracellular pathogen responsible for the most prevalent bacterial sexually transmitted disease globally. The high prevalence of chlamydial infections underscores the urgent need for licensed and effective vaccines to prevent transmission in populations. Bacterial outer membrane vesicles (OMVs) have emerged as promising mucosal vaccine carriers due to their inherent adjuvant properties and the ability to display heterologous antigens. In this proof-of-concept study, we evaluated the immunogenicity of Salmonella OMVs decorated with C. trachomatis MOMP-derived CTH522 or HtrA antigens in mice. Following a prime-boost intranasal vaccination approach, two OMV-based C. trachomatis vaccines elicited significant humoral responses specific to the antigens in both systemic and vaginal compartments. Furthermore, we demonstrated strong antigen-specific IFN-γ and IL17a responses in splenocytes and cervical lymph node cells of vaccinated mice, indicating CD4+ Th1 and Th17 biased immune responses. Notably, the OMV-CTH522 vaccine also induced the production of spleen-derived CD8+ T cells expressing IFN-γ. In conclusion, these results highlight the potential of OMV-based C. trachomatis vaccines for successful use in future challenge studies and demonstrate the suitability of our modular OMV platform for intranasal vaccine applications.
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Affiliation(s)
- Dung T. Huynh
- R&D department, Abera Bioscience AB, Uppsala, Sweden
- Group of Molecular Microbiology, Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Emanuele Nolfi
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Lobna Medfai
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Peter van Ulsen
- Group of Molecular Microbiology, Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | - Alice J. A. M. Sijts
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Joen Luirink
- R&D department, Abera Bioscience AB, Uppsala, Sweden
- Group of Molecular Microbiology, Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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42
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Miniere HJM, Lima EABF, Lorenzo G, Hormuth II DA, Ty S, Brock A, Yankeelov TE. A mathematical model for predicting the spatiotemporal response of breast cancer cells treated with doxorubicin. Cancer Biol Ther 2024; 25:2321769. [PMID: 38411436 PMCID: PMC11057790 DOI: 10.1080/15384047.2024.2321769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 02/18/2024] [Indexed: 02/28/2024] Open
Abstract
Tumor heterogeneity contributes significantly to chemoresistance, a leading cause of treatment failure. To better personalize therapies, it is essential to develop tools capable of identifying and predicting intra- and inter-tumor heterogeneities. Biology-inspired mathematical models are capable of attacking this problem, but tumor heterogeneity is often overlooked in in-vivo modeling studies, while phenotypic considerations capturing spatial dynamics are not typically included in in-vitro modeling studies. We present a data assimilation-prediction pipeline with a two-phenotype model that includes a spatiotemporal component to characterize and predict the evolution of in-vitro breast cancer cells and their heterogeneous response to chemotherapy. Our model assumes that the cells can be divided into two subpopulations: surviving cells unaffected by the treatment, and irreversibly damaged cells undergoing treatment-induced death. MCF7 breast cancer cells were previously cultivated in wells for up to 1000 hours, treated with various concentrations of doxorubicin and imaged with time-resolved microscopy to record spatiotemporally-resolved cell count data. Images were used to generate cell density maps. Treatment response predictions were initialized by a training set and updated by weekly measurements. Our mathematical model successfully calibrated the spatiotemporal cell growth dynamics, achieving median [range] concordance correlation coefficients of > .99 [.88, >.99] and .73 [.58, .85] across the whole well and individual pixels, respectively. Our proposed data assimilation-prediction approach achieved values of .97 [.44, >.99] and .69 [.35, .79] for the whole well and individual pixels, respectively. Thus, our model can capture and predict the spatiotemporal dynamics of MCF7 cells treated with doxorubicin in an in-vitro setting.
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Affiliation(s)
- Hugo J. M. Miniere
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, USA
| | - Ernesto A. B. F. Lima
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, USA
| | - Guillermo Lorenzo
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, USA
- Department of Civil Engineering and Architecture, University of Pavia, Lombardy, Italy
| | - David A. Hormuth II
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, USA
- Livestrong Cancer Institutes, The University of Texas at Austin, Austin, USA
| | - Sophia Ty
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, USA
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, USA
| | - Amy Brock
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, USA
- Livestrong Cancer Institutes, The University of Texas at Austin, Austin, USA
| | - Thomas E. Yankeelov
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, USA
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, USA
- Livestrong Cancer Institutes, The University of Texas at Austin, Austin, USA
- Department of Diagnostic Medicine, The University of Texas at Austin, Austin, USA
- Department of Oncology, The University of Texas at Austin, Austin, USA
- Division of Diagnostic Imaging, The University of Texas M.D. Anderson Cancer Center, Houston, USA
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Yang S, Wang G, Niu M, Zhang H, Ma J, Qu C, Liu G. Impacts of AlaAT3 transgenic poplar on rhizosphere soil chemical properties, enzyme activity, bacterial community, and metabolites under two nitrogen conditions. GM CROPS & FOOD 2024; 15:1-15. [PMID: 38625676 PMCID: PMC11028027 DOI: 10.1080/21645698.2024.2339568] [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: 01/10/2024] [Accepted: 04/02/2024] [Indexed: 04/17/2024]
Abstract
Poplar stands as one of the primary afforestation trees globally. We successfully generated transgenic poplar trees characterized by enhanced biomass under identical nutrient conditions, through the overexpression of the pivotal nitrogen assimilation gene, pxAlaAT3. An environmental risk assessment was conducted for investigate the potential changes in rhizosphere soil associated with these overexpressing lines (OL). The results show that acid phosphatase activity was significantly altered under ammonium in OL compared to the wild-type control (WT), and a similar difference was observed for protease under nitrate. 16SrDNA sequencing indicated no significant divergence in rhizosphere soil microbial community diversity between WT and OL. Metabolomics analysis revealed that the OL caused minimal alterations in the metabolites of the rhizosphere soil, posing no potential harm to the environment. With these findings in mind, we anticipate that overexpressed plants will not adversely impact the surrounding soil environment.
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Affiliation(s)
| | - Gang Wang
- Guizhou Institute of Walnut, Guizhou Academy of Forestry, Guiyang, China
| | - Minghui Niu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Heng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Jing Ma
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Chunpu Qu
- College of Foresty, Guizhou University, Guiyang, China
| | - Guanjun Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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Chen GL, Li JY, Chen X, Liu JW, Zhang Q, Liu JY, Wen J, Wang N, Lei M, Wei JP, Yi L, Li JJ, Ling YP, Yi HQ, Hu Z, Duan J, Zhang J, Zeng B. Mechanosensitive channels TMEM63A and TMEM63B mediate lung inflation-induced surfactant secretion. J Clin Invest 2024; 134:e174508. [PMID: 38127458 PMCID: PMC10904053 DOI: 10.1172/jci174508] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 12/20/2023] [Indexed: 12/23/2023] Open
Abstract
Pulmonary surfactant is a lipoprotein complex lining the alveolar surface to decrease the surface tension and facilitate inspiration. Surfactant deficiency is often seen in premature infants and in children and adults with respiratory distress syndrome. Mechanical stretch of alveolar type 2 epithelial (AT2) cells during lung expansion is the primary physiological factor that stimulates surfactant secretion; however, it is unclear whether there is a mechanosensor dedicated to this process. Here, we show that loss of the mechanosensitive channels TMEM63A and TMEM63B (TMEM63A/B) resulted in atelectasis and respiratory failure in mice due to a deficit of surfactant secretion. TMEM63A/B were predominantly localized at the limiting membrane of the lamellar body (LB), a lysosome-related organelle that stores pulmonary surfactant and ATP in AT2 cells. Activation of TMEM63A/B channels during cell stretch facilitated the release of surfactant and ATP from LBs fused with the plasma membrane. The released ATP evoked Ca2+ signaling in AT2 cells and potentiated exocytic fusion of more LBs. Our study uncovered a vital physiological function of TMEM63 mechanosensitive channels in preparing the lungs for the first breath at birth and maintaining respiration throughout life.
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Affiliation(s)
- Gui-Lan Chen
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
| | - Jing-Yi Li
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
| | - Xin Chen
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
| | - Jia-Wei Liu
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
| | - Qian Zhang
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
| | - Jie-Yu Liu
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
| | - Jing Wen
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
| | - Na Wang
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
| | - Ming Lei
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
| | - Jun-Peng Wei
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
| | - Li Yi
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
| | - Jia-Jia Li
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
| | - Yu-Peng Ling
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
| | - He-Qiang Yi
- Department of Cardiothoracic Surgery, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, Sichuan, China
| | - Zhenying Hu
- Human Aging Research Institute and School of Life Sciences and
| | - Jingjing Duan
- Human Aging Research Institute and School of Life Sciences and
| | - Jin Zhang
- School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Bo Zeng
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
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45
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Hentati D, Ramadan AR, Abed RMM, Abotalib N, El Nayal AM, Ismail W. Functional and structural responses of a halophilic consortium to oily sludge during biodegradation. Appl Microbiol Biotechnol 2024; 108:116. [PMID: 38229295 DOI: 10.1007/s00253-023-12896-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/23/2023] [Accepted: 11/27/2023] [Indexed: 01/18/2024]
Abstract
Biotreatment of oily sludge and the involved microbial communities, particularly in saline environments, have been rarely investigated. We enriched a halophilic bacterial consortium (OS-100) from petroleum refining oily sludge, which degraded almost 86% of the aliphatic hydrocarbon (C10-C30) fraction of the oily sludge within 7 days in the presence of 100 g/L NaCl. Two halophilic hydrocarbon-degrading bacteria related to the genera Chromohalobacter and Halomonas were isolated from the OS-100 consortium. Hydrocarbon degradation by the OS-100 consortium was relatively higher compared to the isolated bacteria, indicating potential synergistic interactions among the OS-100 community members. Exclusion of FeCl2, MgCl2, CaCl2, trace elements, and vitamins from the culture medium did not significantly affect the hydrocarbon degradation efficiency of the OS-100 consortium. To the contrary, hydrocarbon biodegradation dropped from 94.1 to 54.4% and 5% when the OS-100 consortium was deprived from phosphate and nitrogen sources in the culture medium, respectively. Quantitative PCR revealed that alkB gene expression increased up to the 3rd day of incubation with 11.277-fold, consistent with the observed increments in hydrocarbon degradation. Illumina-MiSeq sequencing of 16 S rRNA gene fragments revealed that the OS-100 consortium was mainly composed of the genera Halomonas, Idiomarina, Alcanivorax and Chromohalobacter. This community structure changed depending on the culturing conditions. However, remarkable changes in the community structure were not always associated with remarkable shifts in the hydrocarbonoclastic activity and vice versa. The results show that probably synergistic interactions between community members and different subpopulations of the OS-100 consortium contributed to salinity tolerance and hydrocarbon degradation.
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Affiliation(s)
- Dorra Hentati
- Environmental Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Ahmed R Ramadan
- Health Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Raeid M M Abed
- Biology Department, College of Science, Sultan Qaboos University, Muscat, Oman
| | - Nasser Abotalib
- Environmental Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Ashraf M El Nayal
- Environmental Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Wael Ismail
- Environmental Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain.
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46
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Hu H, Wei XY, Liu L, Wang YB, Bu LK, Jia HJ, Pei DS. Biogeographic patterns of meio- and micro-eukaryotic communities in dam-induced river-reservoir systems. Appl Microbiol Biotechnol 2024; 108:130. [PMID: 38229334 DOI: 10.1007/s00253-023-12993-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 10/30/2023] [Accepted: 12/28/2023] [Indexed: 01/18/2024]
Abstract
Although the Three Gorges Dam (TGD) is the world's largest hydroelectric dam, little is known about the spatial-temporal patterns and community assembly mechanisms of meio- and micro-eukaryotes and its two subtaxa (zooplankton and zoobenthos). This knowledge gap is particularly evident across various habitats and during different water-level periods, primarily arising from the annual regular dam regulation. To address this inquiry, we employed mitochondrial cytochrome c oxidase I (COI) gene-based environmental DNA (eDNA) metabarcoding technology to systematically analyze the biogeographic pattern of the three communities within the Three Gorges Reservoir (TGR). Our findings reveal distinct spatiotemporal characteristics and complementary patterns in the distribution of meio- and micro-eukaryotes. The three communities showed similar biogeographic patterns and assembly processes. Notably, the diversity of these three taxa gradually decreased along the river. Their communities were less shaped by stochastic processes, which gradually decreased along the longitudinal riverine-transition-lacustrine gradient. Hence, deterministic factors, such as seasonality, environmental, and spatial variables, along with species interactions, likely play a pivotal role in shaping these communities. Environmental factors primarily drive seasonal variations in these communities, while hydrological conditions, represented as spatial distance, predominantly influence spatial variations. These three communities followed the distance-decay pattern. In winter, compared to summer, both the decay and species interrelationships are more pronounced. Taken together, this study offers fresh insights into the composition and diversity patterns of meio- and micro-eukaryotes at the spatial-temporal level. It also uncovers the mechanisms behind community assembly in various environmental niches within the dam-induced river-reservoir systems. KEY POINTS: • Distribution and diversity of meio- and micro-eukaryotes exhibit distinct spatiotemporal patterns in the TGR. • Contribution of stochastic processes in community assembly gradually decreases along the river. • Deterministic factors and species interactions shape meio- and micro-eukaryotic community.
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Affiliation(s)
- Huan Hu
- Chongqing Jiaotong University, Chongqing, 400074, China
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Xing-Yi Wei
- Chongqing Jiaotong University, Chongqing, 400074, China
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Li Liu
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Yuan-Bo Wang
- Chongqing Jiaotong University, Chongqing, 400074, China
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Ling-Kang Bu
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China
| | - Huang-Jie Jia
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - De-Sheng Pei
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China.
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47
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Santema LL, Rotilio L, Xiang R, Tjallinks G, Guallar V, Mattevi A, Fraaije MW. Discovery and biochemical characterization of thermostable glycerol oxidases. Appl Microbiol Biotechnol 2024; 108:61. [PMID: 38183484 PMCID: PMC10771423 DOI: 10.1007/s00253-023-12883-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 10/10/2023] [Accepted: 10/20/2023] [Indexed: 01/08/2024]
Abstract
Alditol oxidases are promising tools for the biocatalytic oxidation of glycerol to more valuable chemicals. By integrating in silico bioprospecting with cell-free protein synthesis and activity screening, an effective pipeline was developed to rapidly identify enzymes that are active on glycerol. Three thermostable alditol oxidases from Actinobacteria Bacterium, Streptomyces thermoviolaceus, and Thermostaphylospora chromogena active on glycerol were discovered. The characterization of these three flavoenzymes demonstrated their glycerol oxidation activities, preference for alkaline conditions, and excellent thermostabilities with melting temperatures higher than 75 °C. Structural elucidation of the alditol oxidase from Actinobacteria Bacterium highlighted a constellation of side chains that engage the substrate through several hydrogen bonds, a histidine residue covalently bound to the FAD prosthetic group, and a tunnel leading to the active site. Upon computational simulations of substrate binding, a double mutant targeting a residue pair at the tunnel entrance was created and found to display an improved thermal stability and catalytic efficiency for glycerol oxidation. The hereby described alditol oxidases form a valuable panel of oxidative biocatalysts that can perform regioselective oxidation of glycerol and other polyols. KEY POINTS: • Rapid pipeline designed to identify putative oxidases • Biochemical and structural characterization of alditol oxidases • Glycerol oxidation to more valuable derivatives.
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Affiliation(s)
- Lars L Santema
- Molecular Enzymology, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Laura Rotilio
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Ruite Xiang
- Barcelona Supercomputing Center (BSC), Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, 08034, Spain
| | - Gwen Tjallinks
- Molecular Enzymology, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Victor Guallar
- Barcelona Supercomputing Center (BSC), Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, 08034, Spain.
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, 27100, Pavia, Italy.
| | - Marco W Fraaije
- Molecular Enzymology, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands.
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48
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Qiao Y, Yang R, Liu Y, Chen J, Zhao L, Huo P, Wang Z, Bu D, Wu Y, Zhao Y. DeepFusion: A deep bimodal information fusion network for unraveling protein-RNA interactions using in vivo RNA structures. Comput Struct Biotechnol J 2024; 23:617-625. [PMID: 38274994 PMCID: PMC10808905 DOI: 10.1016/j.csbj.2023.12.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/04/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
RNA-binding proteins (RBPs) are key post-transcriptional regulators, and the malfunctions of RBP-RNA binding lead to diverse human diseases. However, prediction of RBP binding sites is largely based on RNA sequence features, whereas in vivo RNA structural features based on high-throughput sequencing are rarely incorporated. Here, we designed a deep bimodal information fusion network called DeepFusion for unraveling protein-RNA interactions by incorporating structural features derived from DMS-seq data. DeepFusion integrates two sub-models to extract local motif-like information and long-term context information. We show that DeepFusion performs best compared with other cutting-edge methods with only sequence inputs on two datasets. DeepFusion's performance is further improved with bimodal input after adding in vivo DMS-seq structural features. Furthermore, DeepFusion can be used for analyzing RNA degradation, demonstrating significantly different RBP-binding scores in genes with slow degradation rates versus those with rapid degradation rates. DeepFusion thus provides enhanced abilities for further analysis of functional RNAs. DeepFusion's code and data are available at http://bioinfo.org/deepfusion/.
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Affiliation(s)
- Yixuan Qiao
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Yang
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Liu
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaxin Chen
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Lianhe Zhao
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Peipei Huo
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhihao Wang
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Dechao Bu
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Yang Wu
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Yi Zhao
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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49
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Liu X, Wang H, Gao J. scIALM: A method for sparse scRNA-seq expression matrix imputation using the Inexact Augmented Lagrange Multiplier with low error. Comput Struct Biotechnol J 2024; 23:549-558. [PMID: 38274995 PMCID: PMC10809077 DOI: 10.1016/j.csbj.2023.12.027] [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: 10/25/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/27/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) is a high-throughput sequencing technology that quantifies gene expression profiles of specific cell populations at the single-cell level, providing a foundation for studying cellular heterogeneity and patient pathological characteristics. It is effective for developmental, fertility, and disease studies. However, the cell-gene expression matrix of single-cell sequencing data is often sparse and contains numerous zero values. Some of the zero values derive from noise, where dropout noise has a large impact on downstream analysis. In this paper, we propose a method named scIALM for imputation recovery of sparse single-cell RNA data expression matrices, which employs the Inexact Augmented Lagrange Multiplier method to use sparse but clean (accurate) data to recover unknown entries in the matrix. We perform experimental analysis on four datasets, calling the expression matrix after Quality Control (QC) as the original matrix, and comparing the performance of scIALM with six other methods using mean squared error (MSE), mean absolute error (MAE), Pearson correlation coefficient (PCC), and cosine similarity (CS). Our results demonstrate that scIALM accurately recovers the original data of the matrix with an error of 10e-4, and the mean value of the four metrics reaches 4.5072 (MSE), 0.765 (MAE), 0.8701 (PCC), 0.8896 (CS). In addition, at 10%-50% random masking noise, scIALM is the least sensitive to the masking ratio. For downstream analysis, this study uses adjusted rand index (ARI) and normalized mutual information (NMI) to evaluate the clustering effect, and the results are improved on three datasets containing real cluster labels.
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Affiliation(s)
- Xiaohong Liu
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Han Wang
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jingyang Gao
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
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50
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Yan Q, Zhang Y, Hou R, Pan W, Liang H, Gao X, Deng W, Huang X, Qu L, Tang C, He P, Liu B, Wang Q, Zhao X, Lin Z, Chen Z, Li P, Han J, Xiong X, Zhao J, Li S, Niu X, Chen L. Deep immunoglobulin repertoire sequencing depicts a comprehensive atlas of spike-specific antibody lineages shared among COVID-19 convalescents. Emerg Microbes Infect 2024; 13:2290841. [PMID: 38044868 PMCID: PMC10810631 DOI: 10.1080/22221751.2023.2290841] [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: 09/07/2023] [Accepted: 11/29/2023] [Indexed: 12/05/2023]
Abstract
Neutralizing antibodies are a key component in protective humoral immunity against SARS-CoV-2. Currently, available technologies cannot track epitope-specific antibodies in global antibody repertoires. Thus, the comprehensive repertoire of spike-specific neutralizing antibodies elicited by SARS-CoV-2 infection is not fully understood. We therefore combined high-throughput immunoglobulin heavy chain (IgH) repertoire sequencing, and structural and bioinformatics analysis to establish an antibodyomics pipeline, which enables tracking spike-specific antibody lineages that target certain neutralizing epitopes. We mapped the neutralizing epitopes on the spike and determined the epitope-preferential antibody lineages. This analysis also revealed numerous overlaps between immunodominant neutralizing antibody-binding sites and mutation hotspots on spikes as observed so far in SARS-CoV-2 variants. By clustering 2677 spike-specific antibodies with 360 million IgH sequences that we sequenced, a total of 329 shared spike-specific antibody clonotypes were identified from 33 COVID-19 convalescents and 24 SARS-CoV-2-naïve individuals. Epitope mapping showed that the shared antibody responses target not only neutralizing epitopes on RBD and NTD but also non-neutralizing epitopes on S2. The immunodominance of neutralizing antibody response is determined by the occurrence of specific precursors in human naïve B-cell repertoires. We identified that only 28 out of the 329 shared spike-specific antibody clonotypes persisted for at least 12 months. Among them, long-lived IGHV3-53 antibodies are likely to evolve cross-reactivity to Omicron variants through accumulating somatic hypermutations. Altogether, we created a comprehensive atlas of spike-targeting antibody lineages in COVID-19 convalescents and antibody precursors in human naïve B cell repertoires, providing a valuable reference for future vaccine design and evaluation.
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Affiliation(s)
- Qihong Yan
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Yudi Zhang
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- University of Chinese Academy of Science, Beijing, People’s Republic of China
| | - Ruitian Hou
- Guangzhou Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Wenjing Pan
- Hengyang Medical School, University of South China, Hengyang, People’s Republic of China
- Nanjing ARP Biotechnology Co., Ltd, Nanjing, People’s Republic of China
| | - Huan Liang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Xijie Gao
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Weiqi Deng
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- University of Chinese Academy of Science, Beijing, People’s Republic of China
| | - Xiaohan Huang
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Linbing Qu
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Congli Tang
- Nanjing ARP Biotechnology Co., Ltd, Nanjing, People’s Republic of China
| | - Ping He
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Banghui Liu
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Qian Wang
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Xinwei Zhao
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Zihan Lin
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- University of Chinese Academy of Science, Beijing, People’s Republic of China
| | - Zhaoming Chen
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Pingchao Li
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Jian Han
- iRepertoire Inc., Huntsville, AL, USA
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Song Li
- Hengyang Medical School, University of South China, Hengyang, People’s Republic of China
| | - Xuefeng Niu
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Ling Chen
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- Guangzhou Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
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