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Zhou S, Li T, Zhang W, Wu J, Hong H, Quan W, Qiao X, Cui C, Qiao C, Zhao W, Shen Y. The cGAS-STING-interferon regulatory factor 7 pathway regulates neuroinflammation in Parkinson's disease. Neural Regen Res 2025; 20:2361-2372. [PMID: 39359093 DOI: 10.4103/nrr.nrr-d-23-01684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/06/2024] [Indexed: 10/04/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202508000-00026/figure1/v/2024-09-30T120553Z/r/image-tiff Interferon regulatory factor 7 plays a crucial role in the innate immune response. However, whether interferon regulatory factor 7-mediated signaling contributes to Parkinson's disease remains unknown. Here we report that interferon regulatory factor 7 is markedly up-regulated in a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced mouse model of Parkinson's disease and co-localizes with microglial cells. Both the selective cyclic guanosine monophosphate adenosine monophosphate synthase inhibitor RU.521 and the stimulator of interferon genes inhibitor H151 effectively suppressed interferon regulatory factor 7 activation in BV2 microglia exposed to 1-methyl-4-phenylpyridinium and inhibited transformation of mouse BV2 microglia into the neurotoxic M1 phenotype. In addition, siRNA-mediated knockdown of interferon regulatory factor 7 expression in BV2 microglia reduced the expression of inducible nitric oxide synthase, tumor necrosis factor α, CD16, CD32, and CD86 and increased the expression of the anti-inflammatory markers ARG1 and YM1. Taken together, our findings indicate that the cyclic guanosine monophosphate adenosine monophosphate synthase-stimulator of interferon genes-interferon regulatory factor 7 pathway plays a crucial role in the pathogenesis of Parkinson's disease.
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Affiliation(s)
- Shengyang Zhou
- Laboratory of Neurodegenerative and Neuroinjury Diseases, Wuxi Medicine School, Jiangnan University, Wuxi, Jiangsu Province, China
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2
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Yang J, Wu J, Xie X, Xia P, Lu J, Liu J, Bai L, Li X, Yu Z, Li H. Perilipin-2 mediates ferroptosis in oligodendrocyte progenitor cells and myelin injury after ischemic stroke. Neural Regen Res 2025; 20:2015-2028. [PMID: 39254564 DOI: 10.4103/nrr.nrr-d-23-01540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 02/27/2024] [Indexed: 09/11/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202507000-00024/figure1/v/2024-09-09T124005Z/r/image-tiff Differentiation of oligodendrocyte progenitor cells into mature myelin-forming oligodendrocytes contributes to remyelination. Failure of remyelination due to oligodendrocyte progenitor cell death can result in severe nerve damage. Ferroptosis is an iron-dependent form of regulated cell death caused by membrane rupture induced by lipid peroxidation, and plays an important role in the pathological process of ischemic stroke. However, there are few studies on oligodendrocyte progenitor cell ferroptosis. We analyzed transcriptome sequencing data from GEO databases and identified a role of ferroptosis in oligodendrocyte progenitor cell death and myelin injury after cerebral ischemia. Bioinformatics analysis suggested that perilipin-2 (PLIN2) was involved in oligodendrocyte progenitor cell ferroptosis. PLIN2 is a lipid storage protein and a marker of hypoxia-sensitive lipid droplet accumulation. For further investigation, we established a mouse model of cerebral ischemia/reperfusion. We found significant myelin damage after cerebral ischemia, as well as oligodendrocyte progenitor cell death and increased lipid peroxidation levels around the infarct area. The ferroptosis inhibitor, ferrostatin-1, rescued oligodendrocyte progenitor cell death and subsequent myelin injury. We also found increased PLIN2 levels in the peri-infarct area that co-localized with oligodendrocyte progenitor cells. Plin2 knockdown rescued demyelination and improved neurological deficits. Our findings suggest that targeting PLIN2 to regulate oligodendrocyte progenitor cell ferroptosis may be a potential therapeutic strategy for rescuing myelin damage after cerebral ischemia.
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Affiliation(s)
- Jian Yang
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
- Institute of Stroke Research, Soochow University, Suzhou, Jiangsu Province, China
| | - Jiang Wu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
- Institute of Stroke Research, Soochow University, Suzhou, Jiangsu Province, China
| | - Xueshun Xie
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
- Institute of Stroke Research, Soochow University, Suzhou, Jiangsu Province, China
| | - Pengfei Xia
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
- Institute of Stroke Research, Soochow University, Suzhou, Jiangsu Province, China
| | - Jinxin Lu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
- Institute of Stroke Research, Soochow University, Suzhou, Jiangsu Province, China
| | - Jiale Liu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
- Institute of Stroke Research, Soochow University, Suzhou, Jiangsu Province, China
| | - Lei Bai
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
- Institute of Stroke Research, Soochow University, Suzhou, Jiangsu Province, China
| | - Xiang Li
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
- Institute of Stroke Research, Soochow University, Suzhou, Jiangsu Province, China
| | - Zhengquan Yu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
- Institute of Stroke Research, Soochow University, Suzhou, Jiangsu Province, China
| | - Haiying Li
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
- Institute of Stroke Research, Soochow University, Suzhou, Jiangsu Province, China
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3
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Li Q, Liu R, Jing Z, Wei Y, Tu S, Yu H, Gao H, Yuan P. High potential in synergizing the reduction of dissolved organic carbon concentration and carbon dioxide emissions for submerged-vegetation-covered river networks. J Environ Sci (China) 2025; 151:298-309. [PMID: 39481941 DOI: 10.1016/j.jes.2024.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/07/2024] [Accepted: 04/07/2024] [Indexed: 11/03/2024]
Abstract
Various technologies and projects have been explored and developed for the synergetic control of environmental pollution and carbon emissions in aquatic ecosystems. Planting submerged vegetation in shallow waters was also expected to achieve this purpose. However, the magnitude and mechanism of carbon dioxide (CO2) emission affected by submerged vegetation is not clear enough in complex aquatic ecosystems. This study investigated the influences of submerged plants on CO2 emission, ecosystem metabolism features, and microbial community traits based on observations in river networks on the Changjiang River Delta. The results showed that CO2 emission from planted waters accounted for 73% of unplanted waters. Meanwhile, planted waters had higher dissolved organic carbon removal capacity in overlying water and higher potential of carbon sequestration in sediment at the same time. These distinctions between the two habitats were attributed to (1) improved CO2 and bicarbonate consumption in water columns via enhancing photosynthesis and (2) inhibited CO2 production by reconstructing the benthic microbial community. Additional eco-advantages were found in planted sediments, such as a high potential of methane oxidation and xenobiotics biodegradation and a low risk of becoming black and odorous. In brief, submerged vegetation is beneficial in promoting pollution removal and carbon retention synchronously. This study advances our understanding of the feedback between aquatic metabolism and CO2 emission.
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Affiliation(s)
- Qingqian Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China; State Environmental Protection Key Laboratory of Estuarine and Coastal Environment, Chinese Research Academy of Environmental Science, Beijing 100012, China
| | - Ruixia Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China; State Environmental Protection Key Laboratory of Estuarine and Coastal Environment, Chinese Research Academy of Environmental Science, Beijing 100012, China
| | - Zhangmu Jing
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China; State Environmental Protection Key Laboratory of Estuarine and Coastal Environment, Chinese Research Academy of Environmental Science, Beijing 100012, China; State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Yanjie Wei
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China; State Environmental Protection Key Laboratory of Estuarine and Coastal Environment, Chinese Research Academy of Environmental Science, Beijing 100012, China; College of Municipal and Environmental Engineering, Shenyang Jianzhu University, Shenyang 110168, China
| | - Shengqiang Tu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China; State Environmental Protection Key Laboratory of Estuarine and Coastal Environment, Chinese Research Academy of Environmental Science, Beijing 100012, China
| | - Huibin Yu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China; State Environmental Protection Key Laboratory of Estuarine and Coastal Environment, Chinese Research Academy of Environmental Science, Beijing 100012, China
| | - Hongjie Gao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China; State Environmental Protection Key Laboratory of Estuarine and Coastal Environment, Chinese Research Academy of Environmental Science, Beijing 100012, China.
| | - Peng Yuan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China; State Environmental Protection Key Laboratory of Estuarine and Coastal Environment, Chinese Research Academy of Environmental Science, Beijing 100012, China.
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4
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Zhu S, Mao H, Sun S, Yang X, Zhao W, Sheng L, Chen Z. Arbuscular mycorrhizal fungi promote functional gene regulation of phosphorus cycling in rhizosphere microorganisms of Iris tectorum under Cr stress. J Environ Sci (China) 2025; 151:187-199. [PMID: 39481932 DOI: 10.1016/j.jes.2024.02.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 11/03/2024]
Abstract
The mutualistic symbiotic system formed by clumping arbuscular mycorrhizal fungi (AMF) and plants can remediate heavy metal-contaminated soils. However, the specific mechanisms underlying the interaction between AMF and inter-root microbial communities, particularly their impact on organic phosphorus (P) cycling, remain unclear. This study investigated the gene regulation processes involved in inter-root soil phosphorus cycling in wetland plants, specifically Iris tectorum, following inoculation with AMF under varying concentrations of chromium (Cr) stress. Through macro-genome sequencing, we analyzed the composition and structure of the inter-root soil microbial community associated with Iris tectorum under greenhouse pot conditions. The results demonstrated significant changes in the diversity and composition of the inter-root soil microbial community following AMF inoculation, with Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, and Bacteroidetes being the dominant taxa. Under Cr stress, species and gene co-occurrence network analysis revealed that AMF promoted the transformation process of organic phosphorus mineralization and facilitated inorganic phosphorus uptake. Additionally, network analysis of functional genes indicated strong aggregation of (pstS, pstA, pstC, TC.PIT, phoR, pp-gppA) genes, which collectively enhanced phosphorus uptake by plants. These findings shed light on the inter-root soil phosphorus cycling process during the co-remediation of Cr-contaminated soil by AMF-Iris tectorum symbiosis, providing valuable theoretical support for the application of AMF-wetland plant symbiosis systems to remediate heavy metal-contaminated soil.
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Affiliation(s)
- Sixi Zhu
- College of Eco-environment Engineering, Guizhou Minzu University; The Karst Environmental Geological Hazard Prevention of Key Laboratory of State Ethnic Affairs Commission, Guiyang 550025, China.
| | - Huan Mao
- College of Eco-environment Engineering, Guizhou Minzu University; The Karst Environmental Geological Hazard Prevention of Key Laboratory of State Ethnic Affairs Commission, Guiyang 550025, China
| | - Suxia Sun
- College of Eco-environment Engineering, Guizhou Minzu University; The Karst Environmental Geological Hazard Prevention of Key Laboratory of State Ethnic Affairs Commission, Guiyang 550025, China
| | - Xiuqin Yang
- College of Eco-environment Engineering, Guizhou Minzu University; The Karst Environmental Geological Hazard Prevention of Key Laboratory of State Ethnic Affairs Commission, Guiyang 550025, China
| | - Wei Zhao
- College of Eco-environment Engineering, Guizhou Minzu University; The Karst Environmental Geological Hazard Prevention of Key Laboratory of State Ethnic Affairs Commission, Guiyang 550025, China
| | - Luying Sheng
- College of Eco-environment Engineering, Guizhou Minzu University; The Karst Environmental Geological Hazard Prevention of Key Laboratory of State Ethnic Affairs Commission, Guiyang 550025, China
| | - Zhongbing Chen
- Department of Applied Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcka 129, Praha-Suchdol 16500, Czech Republic
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5
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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 PMCID: PMC11438351 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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Wang J, Ran Y, Li Z, Zhao T, Zhang F, Wang J, Liu Z, Chen X. Salsolinol as an RNA m6A methylation inducer mediates dopaminergic neuronal death by regulating YAP1 and autophagy. Neural Regen Res 2025; 20:887-899. [PMID: 38886960 PMCID: PMC11433901 DOI: 10.4103/nrr.nrr-d-23-01592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/18/2024] [Indexed: 06/20/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202503000-00032/figure1/v/2024-06-17T092413Z/r/image-tiff Salsolinol (1-methyl-6,7-dihydroxy-1,2,3,4-tetrahydroisoquinoline, Sal) is a catechol isoquinoline that causes neurotoxicity and shares structural similarity with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine, an environmental toxin that causes Parkinson's disease. However, the mechanism by which Sal mediates dopaminergic neuronal death remains unclear. In this study, we found that Sal significantly enhanced the global level of N6-methyladenosine (m6A) RNA methylation in PC12 cells, mainly by inducing the downregulation of the expression of m6A demethylases fat mass and obesity-associated protein (FTO) and alkB homolog 5 (ALKBH5). RNA sequencing analysis showed that Sal downregulated the Hippo signaling pathway. The m6A reader YTH domain-containing family protein 2 (YTHDF2) promoted the degradation of m6A-containing Yes-associated protein 1 (YAP1) mRNA, which is a downstream key effector in the Hippo signaling pathway. Additionally, downregulation of YAP1 promoted autophagy, indicating that the mutual regulation between YAP1 and autophagy can lead to neurotoxicity. These findings reveal the role of Sal on m6A RNA methylation and suggest that Sal may act as an RNA methylation inducer mediating dopaminergic neuronal death through YAP1 and autophagy. Our results provide greater insights into the neurotoxic effects of catechol isoquinolines compared with other studies and may be a reference for assessing the involvement of RNA methylation in the pathogenesis of Parkinson's disease.
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Affiliation(s)
- Jianan Wang
- Beijing International Science and Technology Cooperation Base for Antiviral Drugs, College of Chemistry and Life, Beijing University of Technology, Beijing, China
| | - Yuanyuan Ran
- Department of Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, China
| | - Zihan Li
- Beijing International Science and Technology Cooperation Base for Antiviral Drugs, College of Chemistry and Life, Beijing University of Technology, Beijing, China
| | - Tianyuan Zhao
- Beijing International Science and Technology Cooperation Base for Antiviral Drugs, College of Chemistry and Life, Beijing University of Technology, Beijing, China
| | - Fangfang Zhang
- Beijing International Science and Technology Cooperation Base for Antiviral Drugs, College of Chemistry and Life, Beijing University of Technology, Beijing, China
| | - Juan Wang
- Beijing International Science and Technology Cooperation Base for Antiviral Drugs, College of Chemistry and Life, Beijing University of Technology, Beijing, China
| | - Zongjian Liu
- Department of Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, China
| | - Xuechai Chen
- Beijing International Science and Technology Cooperation Base for Antiviral Drugs, College of Chemistry and Life, Beijing University of Technology, Beijing, China
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Wang Y, Zhang X, Biverstål H, Bazan NG, Tan S, Li N, Ohshima M, Schultzberg M, Li X. Pro-resolving lipid mediator reduces amyloid-β42-induced gene expression in human monocyte-derived microglia. Neural Regen Res 2025; 20:873-886. [PMID: 38886959 PMCID: PMC11433908 DOI: 10.4103/nrr.nrr-d-23-01688] [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: 10/10/2023] [Revised: 03/25/2024] [Accepted: 05/06/2024] [Indexed: 06/20/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202503000-00031/figure1/v/2024-06-17T092413Z/r/image-tiff Specialized pro-resolving lipid mediators including maresin 1 mediate resolution but the levels of these are reduced in Alzheimer's disease brain, suggesting that they constitute a novel target for the treatment of Alzheimer's disease to prevent/stop inflammation and combat disease pathology. Therefore, it is important to clarify whether they counteract the expression of genes and proteins induced by amyloid-β. With this objective, we analyzed the relevance of human monocyte-derived microglia for in vitro modeling of neuroinflammation and its resolution in the context of Alzheimer's disease and investigated the pro-resolving bioactivity of maresin 1 on amyloid-β42-induced Alzheimer's disease-like inflammation. Analysis of RNA-sequencing data and secreted proteins in supernatants from the monocyte-derived microglia showed that the monocyte-derived microglia resembled Alzheimer's disease-like neuroinflammation in human brain microglia after incubation with amyloid-β42. Maresin 1 restored homeostasis by down-regulating inflammatory pathway related gene expression induced by amyloid-β42 in monocyte-derived microglia, protection of maresin 1 against the effects of amyloid-β42 is mediated by a re-balancing of inflammatory transcriptional networks in which modulation of gene transcription in the nuclear factor-kappa B pathway plays a major part. We pinpointed molecular targets that are associated with both neuroinflammation in Alzheimer's disease and therapeutic targets by maresin 1. In conclusion, monocyte-derived microglia represent a relevant in vitro microglial model for studies on Alzheimer's disease-like inflammation and drug response for individual patients. Maresin 1 ameliorates amyloid-β42-induced changes in several genes of importance in Alzheimer's disease, highlighting its potential as a therapeutic target for Alzheimer's disease.
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Affiliation(s)
- Ying Wang
- Department of Neurobiology, Care Sciences & Society, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
- Department of Neurology, Neuroscience Center, The First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Xiang Zhang
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Biverstål
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Nicolas G. Bazan
- Neuroscience Center of Excellence, Louisiana State University, New Orleans, LA, USA
| | - Shuai Tan
- Department of Medicine, Solna, Clinical Pharmacology Group, Karolinska University Hospital, Stockholm, Sweden
| | - Nailin Li
- Department of Medicine, Solna, Clinical Pharmacology Group, Karolinska University Hospital, Stockholm, Sweden
| | - Makiko Ohshima
- Department of Neurobiology, Care Sciences & Society, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
| | - Marianne Schultzberg
- Department of Neurobiology, Care Sciences & Society, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
| | - Xiaofei Li
- Department of Neurobiology, Care Sciences & Society, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
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8
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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 PMCID: PMC11433896 DOI: 10.4103/nrr.nrr-d-23-01568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/21/2023] [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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9
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Trauer JM, Hughes AE, Shipman DS, Meehan MT, Henderson AS, McBryde ES, Ragonnet R. A data science pipeline applied to Australia's 2022 COVID-19 Omicron waves. Infect Dis Model 2025; 10:99-109. [PMID: 39364337 PMCID: PMC11447346 DOI: 10.1016/j.idm.2024.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 08/04/2024] [Accepted: 08/22/2024] [Indexed: 10/05/2024] Open
Abstract
The field of software engineering is advancing at astonishing speed, with packages now available to support many stages of data science pipelines. These packages can support infectious disease modelling to be more robust, efficient and transparent, which has been particularly important during the COVID-19 pandemic. We developed a package for the construction of infectious disease models, integrated it with several open-source libraries and applied this composite pipeline to multiple data sources that provided insights into Australia's 2022 COVID-19 epidemic. We aimed to identify the key processes relevant to COVID-19 transmission dynamics and thereby develop a model that could quantify relevant epidemiological parameters. The pipeline's advantages include markedly increased speed, an expressive application programming interface, the transparency of open-source development, easy access to a broad range of calibration and optimisation tools and consideration of the full workflow from input manipulation through to algorithmic generation of the publication materials. Extending the base model to include mobility effects slightly improved model fit to data, with this approach selected as the model configuration for further epidemiological inference. Under our assumption of widespread immunity against severe outcomes from recent vaccination, incorporating an additional effect of the main vaccination programs rolled out during 2022 on transmission did not further improve model fit. Our simulations suggested that one in every two to six COVID-19 episodes were detected, subsequently emerging Omicron subvariants escaped 30-60% of recently acquired natural immunity and that natural immunity lasted only one to eight months on average. We documented our analyses algorithmically and present our methods in conjunction with interactive online code notebooks and plots. We demonstrate the feasibility of integrating a flexible domain-specific syntax library with state-of-the-art packages in high performance computing, calibration, optimisation and visualisation to create an end-to-end pipeline for infectious disease modelling. We used the resulting platform to demonstrate key epidemiological characteristics of the transition from the emergency to the endemic phase of the COVID-19 pandemic.
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Affiliation(s)
- James M. Trauer
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Angus E. Hughes
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - David S. Shipman
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Michael T. Meehan
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Australia
| | - Alec S. Henderson
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Australia
| | - Emma S. McBryde
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Australia
| | - Romain Ragonnet
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
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10
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Pan W, Wang Y, Chen G, Ma X, Min Y. A carrier-free nanovaccine combined with cancer immunotherapy overcomes gemcitabine resistance. Biomaterials 2025; 313:122788. [PMID: 39236628 DOI: 10.1016/j.biomaterials.2024.122788] [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: 05/20/2024] [Revised: 08/20/2024] [Accepted: 08/22/2024] [Indexed: 09/07/2024]
Abstract
Drug resistance is a significant challenge in cancer chemotherapy and is a primary factor contributing to poor recovery for cancer patients. Although drug-loaded nanoparticles have shown promise in overcoming chemotherapy resistance, they often carry a combination of drugs and require advanced design and manufacturing processes. Furthermore, they seldom approach chemotherapy-resistant tumors from an immunotherapy perspective. In this study, we developed a therapeutic nanovaccine composed solely of chemotherapy-induced resistant tumor antigens (CIRTAs) and the immune adjuvant Toll-like receptor (TLR) 7/8 agonist R848 (CIRTAs@R848). This nanovaccine does not require additional carriers and has a simple production process. It efficiently delivers antigens and immune stimulants to dendritic cells (DCs) simultaneously, promoting DCs maturation. CIRTAs@R848 demonstrated significant tumor suppression, particularly when used in combination with the immune checkpoint blockade (ICB) anti-PD-1 (αPD-1). The combined therapy increased the infiltration of T cells into the tumor while decreasing the proportion of regulatory T cells (Tregs) and modulating the tumor microenvironment, resulting in long-term immune memory. Overall, this study introduces an innovative strategy for treating chemotherapy-resistant tumors from a novel perspective, with potential applications in personalized immunotherapy and precision medicine.
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Affiliation(s)
- Wen Pan
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China; The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; Department of Bio-X Interdisciplinary Science at Hefei National Laboratory (HFNL) for Physical Science at the Microscale, University of Science and Technology of China, Hefei, 230026, China; CAS Key Lab of Soft Matter Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Yangyi Wang
- Department of General Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Guiyuan Chen
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China; The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; Department of Bio-X Interdisciplinary Science at Hefei National Laboratory (HFNL) for Physical Science at the Microscale, University of Science and Technology of China, Hefei, 230026, China; CAS Key Lab of Soft Matter Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Xiaopeng Ma
- Department of General Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China.
| | - Yuanzeng Min
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China; The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; Department of Bio-X Interdisciplinary Science at Hefei National Laboratory (HFNL) for Physical Science at the Microscale, University of Science and Technology of China, Hefei, 230026, China; CAS Key Lab of Soft Matter Chemistry, University of Science and Technology of China, Hefei, 230026, China.
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11
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Chen Y, Shao Z, Wu S. Research progress on the tsRNA biogenesis, function, and application in lung cancer. Noncoding RNA Res 2025; 10:63-69. [PMID: 39309197 PMCID: PMC11414277 DOI: 10.1016/j.ncrna.2024.09.004] [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: 06/25/2024] [Revised: 08/18/2024] [Accepted: 09/01/2024] [Indexed: 09/25/2024] Open
Abstract
In recent years, there has been a mounting occurrence of lung cancer, which stands as one of the most prevalent malignancies globally. This rise in incidence poses a significant hazard to human health, making lung cancer a matter of grave concern. It has been shown that tRNA-derived small non-coding RNA (tsRNA) is involved in the development of tumors, especially lung cancer, through mechanisms such as regulating mRNA stability, influencing protein translation, and acting as epigenetic regulators. Recent studies have shown that tsRNA is abnormally expressed in the plasma and tissues of lung cancer patients, and its expression level is closely related to the malignancy degree and postoperative recurrence of lung cancer. Therefore, for lung cancer patients, tsRNA represents a promising non-invasive biomarker, exhibiting significant potential for facilitating early diagnosis and prognostic evaluation, and for achieving precision treatment of lung cancer by regulating its expression. This article focuses on the biogenesis of tsRNA and its ability to promote lung cancer cell proliferation and invasion. In addition, the specific clinical significance of tsRNA in lung cancer was discussed. Finally, we discuss the need for further improvement of small RNA sequencing technology, and the future research directions and strategies of tsRNA in lung cancer and tumor diseases were summarized.
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Affiliation(s)
- Yu Chen
- Department of Respiratory Medicine, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, China
- Health Science Center, Ningbo University, Ningbo, Zhejiang, China
| | - Zhuowei Shao
- Department of Respiratory Medicine, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, China
- Health Science Center, Ningbo University, Ningbo, Zhejiang, China
| | - Shibo Wu
- Department of Respiratory Medicine, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, China
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12
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Li G, Gao Q, Li B, Wang J, Cheng B, Wang D, Gao H, Xu W, Wang W, Zhang W, Zhang G, Qi Z, Ji J, Liu Y. Comparative transcriptome profiling reveals the key genes and molecular mechanisms involved in rice under blast infection. Gene 2025; 933:148942. [PMID: 39278376 DOI: 10.1016/j.gene.2024.148942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 09/08/2024] [Accepted: 09/10/2024] [Indexed: 09/18/2024]
Abstract
The aim of this study was to analyze the resistance genes and molecular mechanisms involved in rice blast infection. The contents of seven hormones and eight biochemical indicators in the leaves and spikes were at dynamic levels after inoculation with rice blast strains over time. The mRNA and protein expression of the six genes were consistent with the transcriptome analysis results. In addition, KEGG enrichment analysis showed that Os03g0132000, Os06g0215600, and Os06g0215500 were significantly enriched in the alpha-linolenic acid metabolism KEGG pathway, whereas Os05g0311801 was significantly enriched in the zeatin biosynthesis KEGG pathway. Furthermore, Os03g0180900 and Os09g0439200 were significantly enriched in the plant hormone signal transduction KEGG pathways. Therefore, blast infection could alter the hormones, biochemical indicators, and traits of rice. Moreover, genes including Os03g0132000, Os03g0180900, and Os05g0311801 were identified as rice blast resistance genes, and the mechanism might involve alpha-linolenic acid metabolism, zeatin biosynthesis, and plant hormone signal transduction KEGG pathways.
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Affiliation(s)
- Gang Li
- Huaiyin Institute of Agricultural Science in Xuhuai region of Jiangsu/Huai'an Key Laboratory of Agricultural Biotechnology, Huai'an 223001,China.
| | - Qingsong Gao
- Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection Co-constructed by the Province and Ministry, Huaiyin Normal University, Huai'an 223300, China
| | - Bianhao Li
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, China
| | - Jian Wang
- Huaiyin Institute of Agricultural Science in Xuhuai region of Jiangsu/Huai'an Key Laboratory of Agricultural Biotechnology, Huai'an 223001,China
| | - Baoshan Cheng
- Huaiyin Institute of Agricultural Science in Xuhuai region of Jiangsu/Huai'an Key Laboratory of Agricultural Biotechnology, Huai'an 223001,China
| | - Di Wang
- Huaiyin Institute of Agricultural Science in Xuhuai region of Jiangsu/Huai'an Key Laboratory of Agricultural Biotechnology, Huai'an 223001,China
| | - Hao Gao
- Huaiyin Institute of Agricultural Science in Xuhuai region of Jiangsu/Huai'an Key Laboratory of Agricultural Biotechnology, Huai'an 223001,China
| | - Weijun Xu
- Huaiyin Institute of Agricultural Science in Xuhuai region of Jiangsu/Huai'an Key Laboratory of Agricultural Biotechnology, Huai'an 223001,China
| | - Wei Wang
- Huaiyin Institute of Agricultural Science in Xuhuai region of Jiangsu/Huai'an Key Laboratory of Agricultural Biotechnology, Huai'an 223001,China
| | - Wenxia Zhang
- Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection Co-constructed by the Province and Ministry, Huaiyin Normal University, Huai'an 223300, China
| | - Guoliang Zhang
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, China
| | - Zhongqiang Qi
- Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China
| | - Jianhui Ji
- Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection Co-constructed by the Province and Ministry, Huaiyin Normal University, Huai'an 223300, China.
| | - Yongfeng Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China.
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13
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Xu T, Xu W, Zhang G, Liu Z, Liu H. Characterization of the complete mitochondrial genomes of four tarantulas (Arachnida: Theraphosidae) with phylogenetic analysis. Gene 2025; 933:148954. [PMID: 39303821 DOI: 10.1016/j.gene.2024.148954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Revised: 09/03/2024] [Accepted: 09/17/2024] [Indexed: 09/22/2024]
Abstract
To better understand the evolution of mitochondrial genomes (mitogenomes) within the family Theraphosidae, we characterized mitogenomes of four tarantulas (Grammostola pulchripes, Phormictopus atrichomatus, Pterinochilus murinus and Pterinopelma sazimai) for the first time. The mitogenomes were all classical circular structures, with lengths ranging from 13,822 bp to 14,011 bp. The constitutive genes and the orientation of the coding strand observed in the four mitogenomes were consistent with those found in other species belonging to the Theraphosidae family. The four mitogenomes were compacted and exhibited a preference for A and T, with the rRNA sequences showing a higher A+T content. Ka/Ks and p-distances analyses showed the ND6 gene had highest evolutionary rate, while the COⅠ gene displayed relatively slower evolution. In contrast to previous phylogenetic studies, our phylogenetic analysis based on mitogenomes provides new phylogenetic relationships among subfamilies. Subfamily Theraphosinae is most closely related to Ornithoctoninae, slightly distant from Harpactirinae, and farthest from Selenocosmiinae. The new data we acquired regarding these mitogenomes will aid in understanding the complex interrelationships among species within the Theraphosidae family.
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Affiliation(s)
- Tangjun Xu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Wei Xu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Gaoji Zhang
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Zeyang Liu
- School of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Hongyi Liu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China.
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14
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Li H, Abdullah, Yang H, Guo H, Yuan Y, Ahmed I, Li G, Wang Y, Chang Y, Tian X. Chloroplast genome evolution of Berberis (Berberidaceae): Implications for phylogeny and metabarcoding. Gene 2025; 933:148959. [PMID: 39326472 DOI: 10.1016/j.gene.2024.148959] [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: 06/07/2024] [Revised: 09/07/2024] [Accepted: 09/19/2024] [Indexed: 09/28/2024]
Abstract
Berberidis Radix (Sankezhen), a typical multi-origin Chinese medicinal material, originates from the dried roots of plants of the Berberis genus and is used to treat various ailments. These species have similar morphologies, potentially leading to misidentifications that can impact medicine efficacy. Therefore, developing suitable molecular markers to identify medicinal species is imperative. Furthermore, discrepancies exist in the taxonomy of the Berberis genus. In the present study, we de novo assembled the chloroplast genomes of six Berberis species (Berberis woomungensis C. Y. Wu, Berberis pruinosa Franch., Berberis thunbergii DC., Berberis chinensis Poir., Berberis wilsoniae Hemsl., and Berberis sp.) that commonly constitute Berberidis Radix and compared them with previously reported genomes. Our comparative analysis revealed similarities in genome structure, relative synonymous codon usage, amino acid frequency, repeats, and substitutions. Higher synonymous substitutions, indicative of predominant purifying selection on protein-coding genes, were observed compared to non-synonymous substitutions. However, positive selection was identified in six genes across 29 Berberis species-accD, matK, ndhD, rbcL, ycf1, and ycf2-highlighting their potential roles in adaptive responses to specific environmental conditions within the genus. Inverted repeats expansion and contraction affected the rate of mutations and were associated with the phylogenetic classification of Berberis. Our phylogenetic analysis supported the division of the Berberis complex into four genera, which corroborates previous studies involving extensive sampling. We identified the ndhD-ccsA region as the most polymorphic region and applied this region to Chinese patent medicines containing Berberidis Radix through metabarcoding. The metabarcoding analysis confirmed that five Berberis species commonly constitute Berberidis Radix in Chinese patent medicines. In conclusion, this study provides insight into the molecular evolution of the chloroplast genome and the phylogeny of the Berberis genus. In addition, metabarcoding provides insight into the species composition of Berberidis Radix in Chinese patent medicines.
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Affiliation(s)
- Hui Li
- State Key Laboratory of Chinese Medicine Modernization, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Abdullah
- State Key Laboratory of Chinese Medicine Modernization, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Hongxia Yang
- State Key Laboratory of Chinese Medicine Modernization, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Hua Guo
- State Key Laboratory of Chinese Medicine Modernization, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Ye Yuan
- State Key Laboratory of Chinese Medicine Modernization, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad 45710, Pakistan; Microbiological Analysis Team, Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
| | - Guohui Li
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yu Wang
- State Key Laboratory of Chinese Medicine Modernization, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Yanxu Chang
- State Key Laboratory of Chinese Medicine Modernization, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
| | - Xiaoxuan Tian
- State Key Laboratory of Chinese Medicine Modernization, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
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15
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Narain Singh D, Pandey P, Shankar Singh V, Kumar Tripathi A. Evidence for high-risk pollutants and emerging microbial contaminants at two major bathing ghats of the river Ganga using high-resolution mass spectrometry and metagenomics. Gene 2025; 933:148991. [PMID: 39389327 DOI: 10.1016/j.gene.2024.148991] [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: 05/27/2024] [Revised: 10/01/2024] [Accepted: 10/07/2024] [Indexed: 10/12/2024]
Abstract
An efficient wastewater treatment plant is imperative to limit the entry of emerging pollutants (EPs) and emerging microbial contaminants (EMCs) in the river ecosystem. The detection of emerging EPs in aquatic environments is challenging due to complex sample preparation methods, and the need for sophisticated accurate analytical tools. In Varanasi (India), the river Ganga holds immense significance as a holy river but is consistently polluted with municipal (MWW) and hospital wastewater (HWW). We developed an efficient method for untargeted detection of EPs in the water samples using High-resolution mass spectrometry (HRMS), and identified 577 and 670 chemicals (or chemical components) in the water samples from two major bathing ghats, Assi Ghat (AG) and Dashashwamedh Ghat (DG), respectively. The presence of EPs of different categories viz chemicals from research labs, diagnostic labs, lifestyle and industrial chemicals, toxins, flavor and food additives indicated the unsafe disposal of MWW and HWW or inefficient wastewater treatment plants (WWTPs). Besides, shotgun metagenomic analysis depicted the presence of bacteria associated with MWW viz Cloacibacterium normanse, Sphaerotilus natans (sewage fungi), E. coli, and Prevotella. Also, the presence of human pathogens Arcobacter, Polynucleobacter, Pseudomonas, Klebsiella, Aeromonas, Acinetobacter, Vibrio, and Campylobacter suggests the discharge of HWW. EPs are linked to the development, and transmission of antimicrobial resistance (AMR). Occurrence of antibiotic resistance genes (ARGs), plasmid-borne β-lactamases, aminoglycoside transferases, and ARGs associated with integrons, transposons and plasmids viz mcr-3 gene that confer resistance to colistin, the last resort of antibiotics confirmed the presence of emerging microbial contaminants. Subsequent genome reconstruction studies showed the presence of uncultivable ARB and transmission of ARGs through horizontal gene transfer. This study can be used to monitor the health of aquatic bodies as well as the efficiency of WWTPs and raise an urgent need for efficient WWTPs to safeguard the river, Ganga.
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Affiliation(s)
- Durgesh Narain Singh
- BioNEST-BHU, INNORESTECH FOUNDATION, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Parul Pandey
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Vijay Shankar Singh
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Anil Kumar Tripathi
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India.
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16
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Tao D, Lou S, Huang W, Sun K, Li J, Wang Z, Pi Y, Zhao Y, Wen J, Xie Q, Meng F, Lou G. Clinical and prognostic significance of FBXL6 expression in ovarian cancer. Gene 2025; 933:148978. [PMID: 39368786 DOI: 10.1016/j.gene.2024.148978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 09/24/2024] [Accepted: 09/30/2024] [Indexed: 10/07/2024]
Abstract
OBJECTIVE Growing evidence indicates that F-box and leucine-rich repeat protein 6 (FBXL6) is associated with the progression of various cancers, including gastric cancer, hepatocellular carcinoma, and colorectal cancer. This study focuses on the prognostic significance of FBXL6 in OC. METHODS Differential levels of FBXL6 in multiple cancers were evaluated using the TCGA and GSE26712 databases. We screened FBXL6-related differentially expressed genes using the GSE63885 dataset and conducted Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways analysis. The genes that associate with FBXL6 were screened using the "limma" package, the STRING database, and Cytoscape software, and the association was validated through Gene Expression Profiling Interactive Analysis. The potential substrates of FBXL6 were predicted using UbiBrowser2.0 database. FBXL6 protein levels in 84 OC samples were evaluated using immunohistochemistry. The prognostic significance of FBXL6 was explored using Kaplan-Meier and Cox regression analyses. Based on the Cox regression results, an FBXL6-based nomogram that can predict the overall survival (OS) rate were constructed. Moreover, we examined the net benefits and discriminative ability of the nomogram using the decision curve analysis (DCA), calibration plots, and receiver operating characteristic (ROC) curve. RESULTS FBXL6 was elevated in OC tissues, and the overexpression of FBXL6 was linked to poor prognosis in OC patients. The ROC and DCA curves indicated that the prognostic value of the FBXL6-based nomogram model was superior to that of FBXL6, age, and FIGO stage alone. CONCLUSIONS Elevated FBXL6 expression was an independent factor for OC, and an easily applied nomogram was developed to predict OS in OC patients.
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Affiliation(s)
- Dianxin Tao
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin 150086, PR China
| | - Shenghan Lou
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin 150086, PR China
| | - Wei Huang
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin 150086, PR China
| | - Kaidi Sun
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin 150086, PR China
| | - Jian Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, PR China
| | - Zhiqiang Wang
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin 150086, PR China
| | - Yanan Pi
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin 150086, PR China
| | - Yue Zhao
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin 150086, PR China
| | - Jinglin Wen
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin 150086, PR China
| | - Qin Xie
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin 150086, PR China
| | - Fanling Meng
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin 150086, PR China.
| | - Ge Lou
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin 150086, PR China.
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17
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Baldan F, Demori E, Gnan C, Passon N, Damante G, Mio C, Allegri L, Morgan A, Girotto G, De Paoli F, Limongelli I, Zucca S, Faletra F. Chromoanagenesis of chromosome 22 in a subject with obesity and borderline cognitive performance. Gene 2025; 933:148956. [PMID: 39312981 DOI: 10.1016/j.gene.2024.148956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 09/12/2024] [Accepted: 09/18/2024] [Indexed: 09/25/2024]
Abstract
Chromoanagenesis events consist of complex chromosome rearrangements with multiple breakpoints in one or few chromosomes. Mechanisms of chromoanagenesis are split into three major groups: chromothripsis, chromoanasynthesis and chromoplexy. This study aims to delineate a chromoanagenesis event at the level of chromosome 22 in an individual showing obesity and borderline cognitive performance as major disturbances. The proband and his parents were subjected to conventional karyotyping, CGH array and whole genomic sequencing (WGS). By conventional karyotyping a "de novo" pericentric inversion of chromosome 22 was identified. CGH array identified several imbalances (either deletions or duplications) in the long arm of chromosome 22; the largest is a 4.5 Mb duplication at 22q12.1-22q1.3. The detection of extensive duplications would suggest the occurrence of a chromoanasynthesis event. WGS, in addition to the structural alterations identified by karyotyping and CGH array, revealed two translocations from chromosome 22 to chromosomes 6 and 21 as well as a heterozygous pathogenetic variant of ALMS1 gene; the latter could have contributed to the obesity of our patient. The pericentric inversion induces loss of initial part of TCF20 gene including the 5' regulatory region and the first, noncoding, exon. Heterozygous loss-of-function mutations of TCF20 gene have been found in patients with autism spectrum disorder or intellectual disability, some of them presenting obesity. It is, therefore, possible that disruption of TCF20 gene structure would contribute to a fraction of the patient's phenotype.
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Affiliation(s)
| | - Eliana Demori
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale, Udine, Italy
| | - Chiara Gnan
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale, Udine, Italy
| | - Nadia Passon
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale, Udine, Italy
| | - Giuseppe Damante
- Department of Medicine, University of Udine, Udine, Italy; Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale, Udine, Italy.
| | - Catia Mio
- Department of Medicine, University of Udine, Udine, Italy
| | | | - Anna Morgan
- Institute for Maternal and Child Health-I.R.C.C.S. "Burlo Garofolo", Trieste, Italy
| | - Giorgia Girotto
- Institute for Maternal and Child Health-I.R.C.C.S. "Burlo Garofolo", Trieste, Italy
| | | | | | | | - Flavio Faletra
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale, Udine, Italy
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18
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Musumeci A, Vinci M, Verbinnen I, Treccarichi S, Nigliato E, Chiavetta V, Greco D, Vitello GA, Federico C, Janssens V, Saccone S, Calì F. PPP2R5E: New gene potentially involved in specific learning disorders and myopathy. Gene 2025; 933:148945. [PMID: 39284558 DOI: 10.1016/j.gene.2024.148945] [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: 05/14/2024] [Revised: 09/05/2024] [Accepted: 09/11/2024] [Indexed: 09/21/2024]
Abstract
Protein phosphatase 2A (PP2A) is a family of multifunctional enzymatic complexes crucial for cellular signalling, playing a pivotal role in brain function and development. Mutations in specific genes encoding PP2A complexes have been associated with neurodevelopmental disorders with hypotonia and high risk of seizures. In the current work, we present an individual with specific learning problems, motor coordination disorders, hypotonia and behavioural issues. Although whole exome sequencing (WES) did not unveil pathogenic variants in known genes related to these symptoms, a de novo heterozygous variant Glu191Lys was identified within PPP2R5E, encoding the PP2A regulatory subunit B56ε. The novel variant was not observed in the four healthy brothers and was not detected as parental somatic mosaicism. The mutation predicted a change of charge of the mutated amino acid within a conserved LFDSEDPRER motif common to all PPP2R5 B-subunits. Biochemical assays demonstrated a decreased interaction with the PP2A A and C subunits, leading to disturbances in holoenzyme formation, and thus likely, function. For the first time, we report a potential causal link between the observed variant within the PPP2R5E gene and the symptoms manifested in the subject, spanning specific learning problems and motor coordination disorders potentially associated with myopathy.
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