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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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2
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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 DOI: 10.4103/nrr.nrr-d-23-01688] [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: 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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3
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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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4
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Leuci R, Brunetti L, Tufarelli V, Cerini M, Paparella M, Puvača N, Piemontese L. Role of copper chelating agents: between old applications and new perspectives in neuroscience. Neural Regen Res 2025; 20:751-762. [PMID: 38886940 DOI: 10.4103/nrr.nrr-d-24-00140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/03/2024] [Indexed: 06/20/2024] Open
Abstract
The role of copper element has been an increasingly relevant topic in recent years in the fields of human and animal health, for both the study of new drugs and innovative food and feed supplements. This metal plays an important role in the central nervous system, where it is associated with glutamatergic signaling, and it is widely involved in inflammatory processes. Thus, diseases involving copper (II) dyshomeostasis often have neurological symptoms, as exemplified by Alzheimer's and other diseases (such as Parkinson's and Wilson's diseases). Moreover, imbalanced copper ion concentrations have also been associated with diabetes and certain types of cancer, including glioma. In this paper, we propose a comprehensive overview of recent results that show the importance of these metal ions in several pathologies, mainly Alzheimer's disease, through the lens of the development and use of copper chelators as research compounds and potential therapeutics if included in multi-target hybrid drugs. Seeing how copper homeostasis is important for the well-being of animals as well as humans, we shortly describe the state of the art regarding the effects of copper and its chelators in agriculture, livestock rearing, and aquaculture, as ingredients for the formulation of feed supplements as well as to prevent the effects of pollution on animal productions.
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Affiliation(s)
- Rosalba Leuci
- Department of Pharmacy-Pharmaceutical Science, University of Bari Aldo Moro, Bari, Italy
| | - Leonardo Brunetti
- Department of Pharmacy-Pharmaceutical Science, University of Bari Aldo Moro, Bari, Italy
| | - Vincenzo Tufarelli
- Department of Precision and Regenerative Medicine and Jonian Area (DiMePRe-J), Section of Veterinary Science and Animal Production, University of Bari Aldo Moro, Bari, Italy
| | - Marco Cerini
- Department of Pharmacy-Pharmaceutical Science, University of Bari Aldo Moro, Bari, Italy
| | - Marco Paparella
- Department of Pharmacy-Pharmaceutical Science, University of Bari Aldo Moro, Bari, Italy
| | - Nikola Puvača
- Department of Engineering Management in Biotechnology, Faculty of Economics and Engineering Management in Novi Sad, University Business Academy in Novi Sad, Novi Sad, Serbia
| | - Luca Piemontese
- Department of Pharmacy-Pharmaceutical Science, University of Bari Aldo Moro, Bari, Italy
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5
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Helmold BR, Ahrens A, Fitzgerald Z, Ozdinler PH. Spastin and alsin protein interactome analyses begin to reveal key canonical pathways and suggest novel druggable targets. Neural Regen Res 2025; 20:725-739. [PMID: 38886938 DOI: 10.4103/nrr.nrr-d-23-02068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/05/2024] [Indexed: 06/20/2024] Open
Abstract
Developing effective and long-term treatment strategies for rare and complex neurodegenerative diseases is challenging. One of the major roadblocks is the extensive heterogeneity among patients. This hinders understanding the underlying disease-causing mechanisms and building solutions that have implications for a broad spectrum of patients. One potential solution is to develop personalized medicine approaches based on strategies that target the most prevalent cellular events that are perturbed in patients. Especially in patients with a known genetic mutation, it may be possible to understand how these mutations contribute to problems that lead to neurodegeneration. Protein-protein interaction analyses offer great advantages for revealing how proteins interact, which cellular events are primarily involved in these interactions, and how they become affected when key genes are mutated in patients. This line of investigation also suggests novel druggable targets for patients with different mutations. Here, we focus on alsin and spastin, two proteins that are identified as "causative" for amyotrophic lateral sclerosis and hereditary spastic paraplegia, respectively, when mutated. Our review analyzes the protein interactome for alsin and spastin, the canonical pathways that are primarily important for each protein domain, as well as compounds that are either Food and Drug Administration-approved or are in active clinical trials concerning the affected cellular pathways. This line of research begins to pave the way for personalized medicine approaches that are desperately needed for rare neurodegenerative diseases that are complex and heterogeneous.
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Affiliation(s)
- Benjamin R Helmold
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Angela Ahrens
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Zachary Fitzgerald
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - P Hande Ozdinler
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Molecular Innovation and Drug Discovery, Center for Developmental Therapeutics, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Feinberg School of Medicine, Les Turner ALS Center at Northwestern University, Chicago, IL, USA
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6
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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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7
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Wu B, Liu Y, Li H, Zhu L, Zeng L, Zhang Z, Peng W. Liver as a new target organ in Alzheimer's disease: insight from cholesterol metabolism and its role in amyloid-beta clearance. Neural Regen Res 2025; 20:695-714. [PMID: 38886936 DOI: 10.4103/1673-5374.391305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/07/2023] [Indexed: 06/20/2024] Open
Abstract
Alzheimer's disease, the primary cause of dementia, is characterized by neuropathologies, such as amyloid plaques, synaptic and neuronal degeneration, and neurofibrillary tangles. Although amyloid plaques are the primary characteristic of Alzheimer's disease in the central nervous system and peripheral organs, targeting amyloid-beta clearance in the central nervous system has shown limited clinical efficacy in Alzheimer's disease treatment. Metabolic abnormalities are commonly observed in patients with Alzheimer's disease. The liver is the primary peripheral organ involved in amyloid-beta metabolism, playing a crucial role in the pathophysiology of Alzheimer's disease. Notably, impaired cholesterol metabolism in the liver may exacerbate the development of Alzheimer's disease. In this review, we explore the underlying causes of Alzheimer's disease and elucidate the role of the liver in amyloid-beta clearance and cholesterol metabolism. Furthermore, we propose that restoring normal cholesterol metabolism in the liver could represent a promising therapeutic strategy for addressing Alzheimer's disease.
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Affiliation(s)
- Beibei Wu
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Yuqing Liu
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Hongli Li
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Lemei Zhu
- Academician Workstation, Changsha Medical University, Changsha, Hunan Province, China
| | - Lingfeng Zeng
- Academician Workstation, Changsha Medical University, Changsha, Hunan Province, China
| | - Zhen Zhang
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
- Yangsheng College of Traditional Chinese Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou Province, China
- Qinhuangdao Shanhaiguan Pharmaceutical Co., Ltd, Qinhuangdao, Hebei Province, China
| | - Weijun Peng
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
- National Clinical Research Center for Mental Disorder, The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
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8
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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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9
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Chen J, Zeng X, Wang L, Zhang W, Li G, Cheng X, Su P, Wan Y, Li X. Mutual regulation of microglia and astrocytes after Gas6 inhibits spinal cord injury. Neural Regen Res 2025; 20:557-573. [PMID: 38819067 DOI: 10.4103/nrr.nrr-d-23-01130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 01/17/2024] [Indexed: 06/01/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202502000-00032/figure1/v/2024-05-28T214302Z/r/image-tiff Invasive inflammation and excessive scar formation are the main reasons for the difficulty in repairing nervous tissue after spinal cord injury. Microglia and astrocytes play key roles in the spinal cord injury micro-environment and share a close interaction. However, the mechanisms involved remain unclear. In this study, we found that after spinal cord injury, resting microglia (M0) were polarized into pro-inflammatory phenotypes (MG1 and MG3), while resting astrocytes were polarized into reactive and scar-forming phenotypes. The expression of growth arrest-specific 6 (Gas6) and its receptor Axl were significantly down-regulated in microglia and astrocytes after spinal cord injury. In vitro experiments showed that Gas6 had negative effects on the polarization of reactive astrocytes and pro-inflammatory microglia, and even inhibited the cross-regulation between them. We further demonstrated that Gas6 can inhibit the polarization of reactive astrocytes by suppressing the activation of the Yes-associated protein signaling pathway. This, in turn, inhibited the polarization of pro-inflammatory microglia by suppressing the activation of the nuclear factor-κB/p65 and Janus kinase/signal transducer and activator of transcription signaling pathways. In vivo experiments showed that Gas6 inhibited the polarization of pro-inflammatory microglia and reactive astrocytes in the injured spinal cord, thereby promoting tissue repair and motor function recovery. Overall, Gas6 may play a role in the treatment of spinal cord injury. It can inhibit the inflammatory pathway of microglia and polarization of astrocytes, attenuate the interaction between microglia and astrocytes in the inflammatory microenvironment, and thereby alleviate local inflammation and reduce scar formation in the spinal cord.
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Affiliation(s)
- Jiewen Chen
- Department of Spine Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
- Guangdong Province Key Laboratory of Orthopedics and Traumatology, Guangzhou, Guangdong Province, China
| | - Xiaolin Zeng
- Department of Spine Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
- Guangdong Province Key Laboratory of Orthopedics and Traumatology, Guangzhou, Guangdong Province, China
| | - Le Wang
- Department of Spine Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
- Guangdong Province Key Laboratory of Orthopedics and Traumatology, Guangzhou, Guangdong Province, China
| | - Wenwu Zhang
- Department of Spine Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
- Guangdong Province Key Laboratory of Orthopedics and Traumatology, Guangzhou, Guangdong Province, China
| | - Gang Li
- Department of Spine Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
- Guangdong Province Key Laboratory of Orthopedics and Traumatology, Guangzhou, Guangdong Province, China
| | - Xing Cheng
- Department of Spine Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
- Guangdong Province Key Laboratory of Orthopedics and Traumatology, Guangzhou, Guangdong Province, China
| | - Peiqiang Su
- Department of Spine Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
- Guangdong Province Key Laboratory of Orthopedics and Traumatology, Guangzhou, Guangdong Province, China
| | - Yong Wan
- Department of Spine Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
- Guangdong Province Key Laboratory of Orthopedics and Traumatology, Guangzhou, Guangdong Province, China
| | - Xiang Li
- Department of Spine Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
- Guangdong Province Key Laboratory of Orthopedics and Traumatology, Guangzhou, Guangdong Province, China
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10
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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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11
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Zhao XY, Xu DE, Wu ML, Liu JC, Shi ZL, Ma QH. Regulation and function of endoplasmic reticulum autophagy in neurodegenerative diseases. Neural Regen Res 2025; 20:6-20. [PMID: 38767472 PMCID: PMC11246128 DOI: 10.4103/nrr.nrr-d-23-00995] [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: 06/13/2023] [Revised: 11/09/2023] [Accepted: 12/13/2023] [Indexed: 05/22/2024] Open
Abstract
The endoplasmic reticulum, a key cellular organelle, regulates a wide variety of cellular activities. Endoplasmic reticulum autophagy, one of the quality control systems of the endoplasmic reticulum, plays a pivotal role in maintaining endoplasmic reticulum homeostasis by controlling endoplasmic reticulum turnover, remodeling, and proteostasis. In this review, we briefly describe the endoplasmic reticulum quality control system, and subsequently focus on the role of endoplasmic reticulum autophagy, emphasizing the spatial and temporal mechanisms underlying the regulation of endoplasmic reticulum autophagy according to cellular requirements. We also summarize the evidence relating to how defective or abnormal endoplasmic reticulum autophagy contributes to the pathogenesis of neurodegenerative diseases. In summary, this review highlights the mechanisms associated with the regulation of endoplasmic reticulum autophagy and how they influence the pathophysiology of degenerative nerve disorders. This review would help researchers to understand the roles and regulatory mechanisms of endoplasmic reticulum-phagy in neurodegenerative disorders.
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Affiliation(s)
- Xiu-Yun Zhao
- Department of Neurology and Clinical Research Center of Neurological Disease, the Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
- Institute of Neuroscience & Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, Soochow University, Suzhou, Jiangsu Province, China
| | - De-En Xu
- Department of Neurology, Jiangnan University Medical Center, Wuxi, Jiangsu Province, China
| | - Ming-Lei Wu
- Department of Neurology and Clinical Research Center of Neurological Disease, the Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
- Institute of Neuroscience & Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, Soochow University, Suzhou, Jiangsu Province, China
| | - Ji-Chuan Liu
- Department of Neurology and Clinical Research Center of Neurological Disease, the Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
- Institute of Neuroscience & Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, Soochow University, Suzhou, Jiangsu Province, China
| | - Zi-Ling Shi
- Department of Neurology and Clinical Research Center of Neurological Disease, the Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
- Institute of Neuroscience & Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, Soochow University, Suzhou, Jiangsu Province, China
| | - Quan-Hong Ma
- Department of Neurology and Clinical Research Center of Neurological Disease, the Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
- Institute of Neuroscience & Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, Soochow University, Suzhou, Jiangsu Province, China
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12
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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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13
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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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14
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Jiao F, Meng L, Du K, Li X. The autophagy-lysosome pathway: a potential target in the chemical and gene therapeutic strategies for Parkinson's disease. Neural Regen Res 2025; 20:139-158. [PMID: 38767483 PMCID: PMC11246151 DOI: 10.4103/nrr.nrr-d-23-01195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 12/06/2023] [Indexed: 05/22/2024] Open
Abstract
Parkinson's disease is a common neurodegenerative disease with movement disorders associated with the intracytoplasmic deposition of aggregate proteins such as α-synuclein in neurons. As one of the major intracellular degradation pathways, the autophagy-lysosome pathway plays an important role in eliminating these proteins. Accumulating evidence has shown that upregulation of the autophagy-lysosome pathway may contribute to the clearance of α-synuclein aggregates and protect against degeneration of dopaminergic neurons in Parkinson's disease. Moreover, multiple genes associated with the pathogenesis of Parkinson's disease are intimately linked to alterations in the autophagy-lysosome pathway. Thus, this pathway appears to be a promising therapeutic target for treatment of Parkinson's disease. In this review, we briefly introduce the machinery of autophagy. Then, we provide a description of the effects of Parkinson's disease-related genes on the autophagy-lysosome pathway. Finally, we highlight the potential chemical and genetic therapeutic strategies targeting the autophagy-lysosome pathway and their applications in Parkinson's disease.
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Affiliation(s)
- Fengjuan Jiao
- School of Mental Health, Jining Medical University, Jining, Shandong Province, China
- Shandong Collaborative Innovation Center for Diagnosis, Treatment and Behavioral Interventions of Mental Disorders, Institute of Mental Health, Jining Medical University, Jining, Shandong Province, China
| | - Lingyan Meng
- School of Mental Health, Jining Medical University, Jining, Shandong Province, China
| | - Kang Du
- School of Mental Health, Jining Medical University, Jining, Shandong Province, China
| | - Xuezhi Li
- School of Mental Health, Jining Medical University, Jining, Shandong Province, China
- Shandong Collaborative Innovation Center for Diagnosis, Treatment and Behavioral Interventions of Mental Disorders, Institute of Mental Health, Jining Medical University, Jining, Shandong Province, China
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15
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Li JZ, Ramalingam N, Li S. Targeting epigenetic mechanisms in amyloid-β-mediated Alzheimer's pathophysiology: unveiling therapeutic potential. Neural Regen Res 2025; 20:54-66. [PMID: 38767476 PMCID: PMC11246147 DOI: 10.4103/nrr.nrr-d-23-01827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/07/2024] [Indexed: 05/22/2024] Open
Abstract
Alzheimer's disease is a prominent chronic neurodegenerative condition characterized by a gradual decline in memory leading to dementia. Growing evidence suggests that Alzheimer's disease is associated with accumulating various amyloid-β oligomers in the brain, influenced by complex genetic and environmental factors. The memory and cognitive deficits observed during the prodromal and mild cognitive impairment phases of Alzheimer's disease are believed to primarily result from synaptic dysfunction. Throughout life, environmental factors can lead to enduring changes in gene expression and the emergence of brain disorders. These changes, known as epigenetic modifications, also play a crucial role in regulating the formation of synapses and their adaptability in response to neuronal activity. In this context, we highlight recent advances in understanding the roles played by key components of the epigenetic machinery, specifically DNA methylation, histone modification, and microRNAs, in the development of Alzheimer's disease, synaptic function, and activity-dependent synaptic plasticity. Moreover, we explore various strategies, including enriched environments, exposure to non-invasive brain stimulation, and the use of pharmacological agents, aimed at improving synaptic function and enhancing long-term potentiation, a process integral to epigenetic mechanisms. Lastly, we deliberate on the development of effective epigenetic agents and safe therapeutic approaches for managing Alzheimer's disease. We suggest that addressing Alzheimer's disease may require distinct tailored epigenetic drugs targeting different disease stages or pathways rather than relying on a single drug.
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Affiliation(s)
- Jennie Z Li
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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16
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Takatsuka H, Amari T, Umeda M. Cytokinin signaling is involved in root hair elongation in response to phosphate starvation. PLANT SIGNALING & BEHAVIOR 2024; 19:2305030. [PMID: 38267225 PMCID: PMC10810164 DOI: 10.1080/15592324.2024.2305030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/03/2024] [Indexed: 01/26/2024]
Abstract
Root hair, single-celled tubular structures originating from the epidermis, plays a vital role in the uptake of nutrients from the soil by increasing the root surface area. Therefore, optimizing root hair growth is crucial for plants to survive in fluctuating environments. Root hair length is determined by the action of various plant hormones, among which the roles of auxin and ethylene have been extensively studied. However, evidence for the involvement of cytokinins has remained elusive. We recently reported that the cytokinin-activated B-type response regulators, ARABIDOPSIS RESPONSE REGULATOR 1 (ARR1) and ARR12 directly upregulate the expression of ROOT HAIR DEFECTIVE 6-LIKE 4 (RSL4), which encodes a key transcription factor that controls root hair elongation. However, depending on the nutrient availability, it is unknown whether the ARR1/12-RSL4 pathway controls root hair elongation. This study shows that phosphate deficiency induced the expression of RSL4 and increased the root hair length through ARR1/12, though the transcript and protein levels of ARR1/12 did not change. These results indicate that cytokinins, together with other hormones, regulate root hair growth under phosphate starvation conditions.
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Affiliation(s)
- Hirotomo Takatsuka
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Toshiki Amari
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Masaaki Umeda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama, Ikoma, Nara, Japan
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17
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Kiprono D, Thagun C, Kodama Y. Light-dependent chloroplast relocation in wild strawberry ( Fragaria vesca). PLANT SIGNALING & BEHAVIOR 2024; 19:2342744. [PMID: 38630633 PMCID: PMC11028000 DOI: 10.1080/15592324.2024.2342744] [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: 02/21/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024]
Abstract
Chloroplast photorelocation is a vital organellar response that optimizes photosynthesis in plants amid fluctuating environmental conditions. Chloroplasts exhibit an accumulation response, in which they move toward weak light to enhance photoreception, and an avoidance response, in which they move away from strong light to avoid photodamage. Although chloroplast photorelocation has been extensively studied in model plants such as Arabidopsis thaliana, little is known about this process in the economically important crop strawberry. Here, we investigated chloroplast photorelocation in leaf mesophyll cells of wild strawberry (Fragaria vesca), a diploid relative of commercially cultivated octoploid strawberry (F. × ananassa). Microscopy observation revealed that the periclinal area of leaf mesophyll cells in F. vesca is considerably smaller than that of A. thaliana. Given this small cell size, we investigated chloroplast photorelocation in F. vesca by measuring light transmittance in leaves. Weak blue light induced the accumulation response, whereas strong blue light induced the avoidance response. Unexpectedly, strong red light also induced the accumulation response in F. vesca. These findings shed light on chloroplast photorelocation as an intracellular response, laying the foundation for enhancing photosynthesis and productivity in Fragaria.
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Affiliation(s)
- Daisy Kiprono
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, Japan
- Department of Biological Sciences, School of Pure and Applied Sciences, Meru University of Science and Technology, Meru, Kenya
| | - Chonprakun Thagun
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, Japan
| | - Yutaka Kodama
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, Japan
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18
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Pan S, Zhang Z, Pang W. The causal relationship between bacterial pneumonia and diabetes: a two-sample mendelian randomization study. Islets 2024; 16:2291885. [PMID: 38095344 PMCID: PMC10730180 DOI: 10.1080/19382014.2023.2291885] [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: 08/09/2023] [Accepted: 12/03/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Previous observational studies have established the high prevalence of bacterial pneumonia in diabetic patients, which in turn leads to increased mortality. However, the presence of a causal connection between bacterial pneumonia and diabetes remains unobserved. METHODS We chose genome-wide significant (Ρ < 1 × 10-5 and Ρ < 1 × 10-6) and independent (r2 < 0.001) single-nucleotide polymorphisms (SNPs) as instrumental variables (IVs) to proceed a bidirectional two-sample MR study. The extracted SNPs explored the relationship between bacterial pneumonia and diabetes by Inverse variance weighted (IVW), MR-Egger, and weighted median methods. In addition, we conducted the Heterogeneity test, the Pleiotropy test, MR-presso and the Leave-one-out (LOO) sensitivity test to validate the reliability of results. RESULTS In an MR study with bacterial pneumonia as an exposure factor, four different types of diabetes as outcome. It was observed that bacterial pneumonia increases the incidence of GDM (OR = 1.150 (1.027-1.274, P = 0.011) and T1DM (OR = 1.277 (1.024-1.531), P = 0.016). In the reverse MR analysis, it was observed that GDM (OR = 1.112 (1.023-1.201, P = 0.009) is associated with an elevated risk of bacterial pneumonia. However, no significant association was observed bacterial pneumonia with T1DM and other types of diabetes (P > 0.05). CONCLUSION This study utilizing MR methodology yields robust evidence supporting a bidirectional causal association between bacterial pneumonia and GDM. Furthermore, our findings suggest a plausible causal link between bacterial pneumonia and T1DM.
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Affiliation(s)
- Songying Pan
- The School of Public Health, Guilin Medical University, Guilin, Guangxi, China
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guilin Medical University, Guilin, Guangxi, China
| | - Zhongqi Zhang
- The School of Public Health, Guilin Medical University, Guilin, Guangxi, China
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guilin Medical University, Guilin, Guangxi, China
| | - Weiyi Pang
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guilin Medical University, Guilin, Guangxi, China
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19
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Jain SM, Nagainallur Ravichandran S, Murali Kumar M, Banerjee A, Sun-Zhang A, Zhang H, Pathak R, Sun XF, Pathak S. Understanding the molecular mechanism responsible for developing therapeutic radiation-induced radioresistance of rectal cancer and improving the clinical outcomes of radiotherapy - A review. Cancer Biol Ther 2024; 25:2317999. [PMID: 38445632 PMCID: PMC10936619 DOI: 10.1080/15384047.2024.2317999] [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: 08/16/2023] [Accepted: 02/08/2024] [Indexed: 03/07/2024] Open
Abstract
Rectal cancer accounts for the second highest cancer-related mortality, which is predominant in Western civilizations. The treatment for rectal cancers includes surgery, radiotherapy, chemotherapy, and immunotherapy. Radiotherapy, specifically external beam radiation therapy, is the most common way to treat rectal cancer because radiation not only limits cancer progression but also significantly reduces the risk of local recurrence. However, therapeutic radiation-induced radioresistance to rectal cancer cells and toxicity to normal tissues are major drawbacks. Therefore, understanding the mechanistic basis of developing radioresistance during and after radiation therapy would provide crucial insight to improve clinical outcomes of radiation therapy for rectal cancer patients. Studies by various groups have shown that radiotherapy-mediated changes in the tumor microenvironment play a crucial role in developing radioresistance. Therapeutic radiation-induced hypoxia and functional alterations in the stromal cells, specifically tumor-associated macrophage (TAM) and cancer-associated fibroblasts (CAF), play a crucial role in developing radioresistance. In addition, signaling pathways, such as - the PI3K/AKT pathway, Wnt/β-catenin signaling, and the hippo pathway, modulate the radiation responsiveness of cancer cells. Different radiosensitizers, such as small molecules, microRNA, nanomaterials, and natural and chemical sensitizers, are being used to increase the effectiveness of radiotherapy. This review highlights the mechanism responsible for developing radioresistance of rectal cancer following radiotherapy and potential strategies to enhance the effectiveness of radiotherapy for better management of rectal cancer.
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Affiliation(s)
- Samatha M Jain
- Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Chettinad Hospital and Research Institute, Kelambakkam, Chennai, India
| | - Shruthi Nagainallur Ravichandran
- Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Chettinad Hospital and Research Institute, Kelambakkam, Chennai, India
| | - Makalakshmi Murali Kumar
- Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Chettinad Hospital and Research Institute, Kelambakkam, Chennai, India
| | - Antara Banerjee
- Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Chettinad Hospital and Research Institute, Kelambakkam, Chennai, India
| | - Alexander Sun-Zhang
- Department of Oncology-Pathology, BioClinicum, Karolinska Institutet, Stockholm, Sweden
| | - Hong Zhang
- School of Medicine, Department of Medical Sciences, Orebro University, Örebro, Sweden
| | - Rupak Pathak
- Division of Radiation Health, Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Xiao-Feng Sun
- Department of Oncology and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Surajit Pathak
- Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Chettinad Hospital and Research Institute, Kelambakkam, Chennai, India
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20
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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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21
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Evans ST, Jani Y, Jansen CS, Yildirim A, Kalemoglu E, Bilen MA. Understanding and overcoming resistance to immunotherapy in genitourinary cancers. Cancer Biol Ther 2024; 25:2342599. [PMID: 38629578 PMCID: PMC11028033 DOI: 10.1080/15384047.2024.2342599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024] Open
Abstract
The introduction of novel immunotherapies has significantly transformed the treatment landscape of genitourinary (GU) cancers, even becoming the standard of care in some settings. One such type of immunotherapy, immune checkpoint inhibitors (ICIs) like nivolumab, ipilimumab, pembrolizumab, and atezolizumab play a pivotal role by disturbing signaling pathways that limit the immune system's ability to fight tumor cells. Despite the profound impact of these treatments, not all tumors are responsive. Recent research efforts have been focused on understanding how cancer cells manage to evade the immune response and identifying the possible mechanisms behind resistance to immunotherapy. In response, ICIs are being combined with other treatments to reduce resistance and attack cancer cells through multiple cellular pathways. Additionally, novel, targeted strategies are currently being investigated to develop innovative methods of overcoming resistance and treatment failure. This article presents a comprehensive overview of the mechanisms of immunotherapy resistance in GU cancers as currently described in the literature. It explores studies that have identified genetic markers, cytokines, and proteins that may predict resistance or response to immunotherapy. Additionally, we review current efforts to overcome this resistance, which include combination ICIs and sequential therapies, novel insights into the host immune profile, and new targeted therapies. Various approaches that combine immunotherapy with chemotherapy, targeted therapy, vaccines, and radiation have been studied in an effort to more effectively overcome resistance to immunotherapy. While each of these combination therapies has shown some efficacy in clinical trials, a deeper understanding of the immune system's role underscores the potential of novel targeted therapies as a particularly promising area of current research. Currently, several targeted agents are in development, along with the identification of key immune mediators involved in immunotherapy resistance. Further research is necessary to identify predictors of response.
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Affiliation(s)
- Sean T Evans
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Yash Jani
- Undergraduate studies, Mercer University, Macon, GA, USA
| | - Caroline S Jansen
- Medical Scientist Training Program, Emory University School of Medicine, Atlanta, GA, USA
- Genitourinary Medical Oncology Program, Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Ahmet Yildirim
- Genitourinary Medical Oncology Program, Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA
| | - Ecem Kalemoglu
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Department of Basic Oncology, Health Institute of Ege University, Izmir, Turkey
| | - Mehmet Asim Bilen
- Genitourinary Medical Oncology Program, Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA
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22
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Yang X, Wei J, Sun L, Zhong Q, Zhai X, Chen Y, Luo S, Tang C, Wang L. Causal relationship between iron status and preeclampsia-eclampsia: a Mendelian randomization analysis. Clin Exp Hypertens 2024; 46:2321148. [PMID: 38471132 DOI: 10.1080/10641963.2024.2321148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/15/2024] [Indexed: 03/14/2024]
Abstract
BACKGROUND Preeclampsia/eclampsia is a severe pregnancy-related disorder associated with hypertension and organ damage. While observational studies have suggested a link between maternal iron status and preeclampsia/eclampsia, the causal relationship remains unclear. The aim of this study was to investigate the genetic causality between iron status and preeclampsia/eclampsia using large-scale genome-wide association study (GWAS) summary data and Mendelian randomization (MR) analysis. METHODS Summary data for the GWAS on preeclampsia/eclampsia and genetic markers related to iron status were obtained from the FinnGen Consortium and the IEU genetic databases. The "TwoSampleMR" software package in R was employed to test the genetic causality between these markers and preeclampsia/eclampsia. The inverse variance weighted (IVW) method was primarily used for MR analysis. Heterogeneity, horizontal pleiotropy, and potential outliers were evaluated for the MR analysis results. RESULTS The random-effects IVW results showed that ferritin (OR = 1.11, 95% CI: .89-1.38, p = .341), serum iron (OR = .90, 95% CI: .75-1.09, p = .275), TIBC (OR = .98, 95% CI: .89-1.07, p = .613), and TSAT (OR = .94, 95% CI: .83-1.07, p = .354) have no genetic causal relationship with preeclampsia/eclampsia. There was no evidence of heterogeneity, horizontal pleiotropy, or possible outliers in our MR analysis (p > .05). CONCLUSIONS Our study did not detect a genetic causal relationship between iron status and preeclampsia/eclampsia. Nonetheless, this does not rule out a relationship between the two at other mechanistic levels.
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Affiliation(s)
- Xiaofeng Yang
- Department of Obstetrics and Gynecology, Chongqing Health Center for Women and Children, Chongqing, China
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Jiachun Wei
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Lu Sun
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Qimei Zhong
- Department of Obstetrics and Gynecology, Chongqing Health Center for Women and Children, Chongqing, China
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaoxuan Zhai
- Department of Obstetrics and Gynecology, Chongqing Health Center for Women and Children, Chongqing, China
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Ya Chen
- Department of Obstetrics and Gynecology, Chongqing Health Center for Women and Children, Chongqing, China
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Shujuan Luo
- Department of Obstetrics and Gynecology, Chongqing Health Center for Women and Children, Chongqing, China
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Chunyan Tang
- Department of Obstetrics and Gynecology, Chongqing Health Center for Women and Children, Chongqing, China
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Lan Wang
- Department of Obstetrics and Gynecology, Chongqing Health Center for Women and Children, Chongqing, China
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
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23
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Du Q, Zhang M, Gao A, He T, Guo M. Epigenetic silencing ZSCAN23 promotes pancreatic cancer growth by activating Wnt signaling. Cancer Biol Ther 2024; 25:2302924. [PMID: 38226836 PMCID: PMC10793710 DOI: 10.1080/15384047.2024.2302924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/04/2024] [Indexed: 01/17/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most malignant tumor. Zinc finger and SCAN domain-containing protein 23 (ZSCAN23) is a new member of the SCAN domain family. The expression regulation and biological function remain to be elucidated. In this study, we explored the epigenetic regulation and the function of ZSCAN23 in PDAC. ZSCAN23 was methylated in 60.21% (171/284) of PDAC and its expression was regulated by promoter region methylation. The expression of ZSCAN23 inhibited cell proliferation, colony formation, migration, invasion, and induced apoptosis and G1/S phase arrest. ZSCAN23 suppressed Panc10.05 cell xenograft growth in mice. Mechanistically, ZSCAN23 inhibited Wnt signaling by interacting with myosin heavy chain 9 (MYH9) in pancreatic cancer cells. ZSCAN23 is frequently methylated in PDAC and may serve as a detective marker. ZSCAN23 suppresses PDAC cell growth both in vitro and in vivo.
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Affiliation(s)
- Qian Du
- Department of Gastroenterology and Hepatology, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, People's Republic of China
- Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Meiying Zhang
- Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Aiai Gao
- Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Tao He
- Department of Pathology, Characteristic Medical Center of the Chinese People's Armed Police Force, Tianjin, People's Republic of China
| | - Mingzhou Guo
- Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
- National Key Laboratory of Kidney Diseases, the First Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
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24
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Lefler DS, Manobianco SA, Bashir B. Immunotherapy resistance in solid tumors: mechanisms and potential solutions. Cancer Biol Ther 2024; 25:2315655. [PMID: 38389121 PMCID: PMC10896138 DOI: 10.1080/15384047.2024.2315655] [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: 07/24/2023] [Accepted: 02/04/2024] [Indexed: 02/24/2024] Open
Abstract
While the emergence of immunotherapies has fundamentally altered the management of solid tumors, cancers exploit many complex biological mechanisms that result in resistance to these agents. These encompass a broad range of cellular activities - from modification of traditional paradigms of immunity via antigen presentation and immunoregulation to metabolic modifications and manipulation of the tumor microenvironment. Intervening on these intricate processes may provide clinical benefit in patients with solid tumors by overcoming resistance to immunotherapies, which is why it has become an area of tremendous research interest with practice-changing implications. This review details the major ways cancers avoid both natural immunity and immunotherapies through primary (innate) and secondary (acquired) mechanisms of resistance, and it considers available and emerging therapeutic approaches to overcoming immunotherapy resistance.
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Affiliation(s)
- Daniel S. Lefler
- Department of Medicine, Division of Hematology and Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Steven A. Manobianco
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Babar Bashir
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
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25
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Bonato B, Simonetti V, Guerra S, Castiello U. Artificial and biological supports are different for pea plants. PLANT SIGNALING & BEHAVIOR 2024; 19:2355739. [PMID: 38837041 PMCID: PMC7616103 DOI: 10.1080/15592324.2024.2355739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/08/2024] [Indexed: 06/06/2024]
Abstract
Previous studies on the kinematics of pea plants' ascent and attach behavior have demonstrated that the signature of their movement varies depending on the kind of support. So far, these studies have been confined to artificial supports (e.g. wooden sticks). Little is known regarding the conditions under which pea plants could rely on biological supports (e.g. neighboring plants) for climbing toward the light. In this study, we capitalize on the 3D kinematic analysis of movement to ascertain whether pea plants scale their kinematics differently depending on whether they aim for artificial or biological support. Results suggest that biological support determines a smoother and more accurate behavior than that elicited by the artificial one. These results shed light on pea plants' ability to detect and classify the properties of objects and implement a movement plan attuned to the very nature of the support. We contend that such differences depend on the augmented multisensory experience elicited by the biological support.
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Affiliation(s)
- Bianca Bonato
- Department of General Psychology, University of Padova, Padova, Italy
| | | | - Silvia Guerra
- Department of General Psychology, University of Padova, Padova, Italy
| | - Umberto Castiello
- Department of General Psychology, University of Padova, Padova, Italy
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26
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Lehrich BM, Delgado ER. Lipid Nanovesicle Platforms for Hepatocellular Carcinoma Precision Medicine Therapeutics: Progress and Perspectives. Organogenesis 2024; 20:2313696. [PMID: 38357804 PMCID: PMC10878025 DOI: 10.1080/15476278.2024.2313696] [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: 07/06/2023] [Accepted: 01/30/2024] [Indexed: 02/16/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related mortality globally. HCC is highly heterogenous with diverse etiologies leading to different driver mutations potentiating unique tumor immune microenvironments. Current therapeutic options, including immune checkpoint inhibitors and combinations, have achieved limited objective response rates for the majority of patients. Thus, a precision medicine approach is needed to tailor specific treatment options for molecular subsets of HCC patients. Lipid nanovesicle platforms, either liposome- (synthetic) or extracellular vesicle (natural)-derived present are improved drug delivery vehicles which may be modified to contain specific cargos for targeting specific tumor sites, with a natural affinity for liver with limited toxicity. This mini-review provides updates on the applications of novel lipid nanovesicle-based therapeutics for HCC precision medicine and the challenges associated with translating this therapeutic subclass from preclinical models to the clinic.
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Affiliation(s)
- Brandon M. Lehrich
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Medical Scientist Training Program, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Evan R. Delgado
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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27
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Zhu Z, Geng Y, Ma L, Yao K, Chang R, Ma Y, Li J. Association between CBS gene T833C, G919A and 844ins68 polymorphisms in the 8th exon region and coronary artery disease: a meta-analysis. Clin Exp Hypertens 2024; 46:2328147. [PMID: 38488417 DOI: 10.1080/10641963.2024.2328147] [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: 06/02/2023] [Accepted: 03/01/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND Several studies indicate that the cystathionine β-synthase (CBS) gene T833C, G919A and 844ins68 polymorphisms in the 8th exon region may be correlated with coronary artery disease (CAD) susceptibility, but the results have been inconsistent and inconclusive. Thus, a meta-analysis was conducted to provide a comprehensive estimate of these associations. METHODS On the basis of searches in the PubMed, EMBASE, Cochrane Library, Wanfang, VIP, and CNKI databases, we selected 14 case - control studies including 2123 cases and 2368 controls for this meta-analysis. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were calculated accordingly using a fixed-effect or random-effect model. RESULTS The results indicated an increased risk between the CBS T833C gene polymorphisms and susceptibility to CAD under the dominant model (CC+CT vs. TT: OR = 1.92, 95% CI: 1.11 ~ 3.32), recessive model (CC vs. CT+TT: OR = 1.88, 95% CI: 1.17 ~ 3.03), and homozygous model (CC vs. TT: OR = 2.46, 95% CI: 1.04 ~ 5.83). In these three genetic models, no significant association was identified for CBS G919A (AA+AG vs. GG: OR = 1.48, 95% CI: 0.45 ~ 4.82),(AA vs. AG+GG: OR = 1.58, 95% CI: 0.93 ~ 2.70),(AA vs. GG: OR = 1.66, 95% CI: 0.40 ~ 6.92) or CBS 844ins68 (II+ID vs. DD: OR = 1.04, 95% CI: 0.80 ~ 1.35),(II vs. ID+DD: OR = 1.09, 95% CI: 0.51 ~ 2.36),(II vs. DD: OR = 1.10, 95% CI: 0.51 ~ 2.39). CONCLUSIONS This meta-analysis suggests that the CBS T833C gene polymorphism is significantly associated with the risk of CAD and it shows a stronger association in Asian populations. Individuals with the C allele of the CBS gene T833C polymorphism might be particularly susceptible to CAD.
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Affiliation(s)
- Zijiang Zhu
- Department of thoracic surgery, Gansu Provincial Central Hospital (Gansu Provincial Maternity and Child-care Hospital), Lanzhou, China
| | - Yuhan Geng
- School of Clinical Medicine, Ningxia Medical University, Yinchuan, China
| | - Long Ma
- Department of thoracic surgery, Gansu Provincial Central Hospital (Gansu Provincial Maternity and Child-care Hospital), Lanzhou, China
- Department of thoracic surgery, Gansu University of Chinese Medicine, Lanzhou, China
| | - Keying Yao
- School of Second Clinical Medical, Lanzhou University, Lanzhou, China
| | - Ruitong Chang
- Department of thoracic surgery, Gansu Provincial Central Hospital (Gansu Provincial Maternity and Child-care Hospital), Lanzhou, China
| | - Yongming Ma
- Department of thoracic surgery, Gansu Provincial Central Hospital (Gansu Provincial Maternity and Child-care Hospital), Lanzhou, China
- Department of thoracic surgery, Gansu University of Chinese Medicine, Lanzhou, China
| | - Jialong Li
- Department of thoracic surgery, Gansu Provincial Central Hospital (Gansu Provincial Maternity and Child-care Hospital), Lanzhou, China
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28
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Han L, Liu J, Shataer M, Wu C, Niyazi M. The relationship between long non-coding gene CASC21 polymorphisms and cervical cancer. Cancer Biol Ther 2024; 25:2322207. [PMID: 38465665 PMCID: PMC10936591 DOI: 10.1080/15384047.2024.2322207] [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: 05/25/2023] [Accepted: 02/19/2024] [Indexed: 03/12/2024] Open
Abstract
BACKGROUND CASC21 was reported to be a hotspot gene in cervical cancer. The relationship between CASC21 genetic polymorphisms and cervical cancer has not been reported. Genetic factors influence the occurrence of cervical cancer. Thus, we explored the correlation between CASC21 polymorphisms and cervical cancer. METHODS A total of 973 participants within 494 cervical cancer cases and 479 healthy controls were recruited. Five single nucleotide polymorphisms (SNPs) in the CASC21 gene were genotyped using the Agena MassARRAY platform. Chi-squared test, logistic regression analysis, odds ratio (OR), multifactor dimensionality reduction (MDR), and 95% confidence interval (95%CI) were used for data analysis. RESULTS In the overall analysis, rs16902094 (p = .014, OR = 1.86, 95% CI = 1.12-3.08) and rs16902104 (p = .014, OR = 1.86, 95% CI = 1.12-3.09) had the risk-increasing correlation with the occurrence of cervical cancer. Stratification analysis showed that rs16902094 and rs16902104 were still associated with cervical cancer risk in the subgroups with age > 51, BMI < 24 kg/m2, smokers, and patients with cervical squamous cell carcinoma. MDR analysis displayed that rs16902094 (.49%) and rs16902104 (.52%) were the main influential attribution factor for cervical cancer risk. CONCLUSION Our finding firstly determined that two CASC21 SNPs (rs16902094, rs16902104) were associated with an increased risk of cervical cancer, which adds to our knowledge regarding the effect of CASC21 on cervical carcinogenesis.
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Affiliation(s)
- Lili Han
- Department of Gynecology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumchi, Xinjiang, China
| | - Jing Liu
- Department of Gynecology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumchi, Xinjiang, China
| | - Mireayi Shataer
- Department of Gynecology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumchi, Xinjiang, China
| | - Chengyong Wu
- Department of Gynecology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumchi, Xinjiang, China
| | - Mayinuer Niyazi
- Department of Gynecology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumchi, Xinjiang, China
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29
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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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30
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Zhao X, Gao Q, Wang H, Yue J, An D, Li B, Yan F, Carmen SM, Zhao Y, Zhou H, Zhao M. syn-tasiRnas targeting the coat protein of potato virus Y confer antiviral resistance in Nicotiana benthamiana. PLANT SIGNALING & BEHAVIOR 2024; 19:2358270. [PMID: 38796845 PMCID: PMC11135832 DOI: 10.1080/15592324.2024.2358270] [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: 03/31/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024]
Abstract
Trans-acting small interfering RNAs (tasiRNAs) are 21-nt phased (phased siRNAs) resulting from successive DCL-catalyzed processing from the end of a double-stranded RNA substrate originating from the RDR of an AGO-catalyzed cleaved RNA at a micro RNA target site. Plant tasiRNAs have been synthesized to produce synthetic tasiRNAs (syn-tasiRNAs) targeting viral RNAs that confer viral resistance. In this study, we engineered syn-tasiRNAs to target potato virus Y (PVY) infection by replacing five native siRNAs of TAS1c with 210-bp fragments from the coat protein (CP) region of the PVY genome. The results showed that the transient expression of syn-tasiR-CPpvy2 in Nicotiana benthamiana (N. benthamiana) plants conferred antiviral resistance, supported by the absence of PVY infection symptoms and viral accumulation. This indicated that syn-tasiR-CPpvy2 successfully targeted and silenced the PVY CP gene, effectively inhibiting viral infection. syn-tasiR-CPpvy1 displayed attenuated symptoms and decreased viral accumulation in these plants However, severe symptoms of PVY infection and a similar amount of viral accumulation as the control were observed in plants expressing syn-tasiR-CPpvy3. syn-tasiR-CPpvy/pvx, which targets both PVY and potato virus X (PVX), was engineered using a single precursor. After the transient expression of syn-tasiR-CPpvy/pvx3 and syn-tasiR-CPpvy/pvx5 in N. benthamiana, the plants were resistant to both PVY and PVX. These results suggested that engineered syn-tasiRNAs could not only specifically induce antiviral resistance against one target virus but could also be designed for multi-targeted silencing of different viruses, thereby preventing complex virus infection in plants.
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Affiliation(s)
- Xingyue Zhao
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Qian Gao
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Haijuan Wang
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Jianying Yue
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Derong An
- College of Plant Protection, Northwest A&F University, Yangling, China
| | - Bin Li
- Department of Tabacco Production, Sichuan Province Company of Tobacco Corporation in China, Chengdu, China
| | - Fangfang Yan
- Panzhihua City company of Sichuan province company of Tobacco Corporation in China, Panzhihua city, Sichuan provience, China
| | | | - Yuanzheng Zhao
- Department of Plant Protection, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Hongyou Zhou
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Mingmin Zhao
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
- Department of Plant protection, Key Laboratory of the Development and Resource Utilization of Biological Pesticide in Inner Mongolia, Hohhot, China
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Jiang H, Zhang Y, Li J, Tang R, Liang F, Tang R, Zhou Y, Zhang C. Genome-wide identification of SIMILAR to RCD ONE (SRO) gene family in rapeseed ( Brassica napus L.) reveals their role in drought stress response. PLANT SIGNALING & BEHAVIOR 2024; 19:2379128. [PMID: 39003725 PMCID: PMC11249032 DOI: 10.1080/15592324.2024.2379128] [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: 04/03/2024] [Accepted: 05/22/2024] [Indexed: 07/16/2024]
Abstract
Rapeseed (Brassica napus L.) is an important oilseed crop widely cultivated worldwide, and drought is the main environmental factor limiting its yield enhancement and the expansion of planted areas. SIMILAR TO RCD ONE (SRO) is a plant-specific small gene family that plays a crucial role in plant growth, development, and responses to abiotic stresses such as drought. However, the functional role of SROs in rapeseed remains poorly understood. In this study, 19 BnaSROs were identified from the rapeseed genome, with 9, 10, 10, 18, and 20 members identified from the genomes of Brassica rapa, Brassica nigra, Brassica oleracea, Brassica juncea, and Brassica carinata, respectively. We then analyzed their sequence characteristics, phylogenetic relationships, gene structures, and conserved domains, and explored the collinearity relationships of the SRO members in Brassica napus and Brassica juncea. Next, we focused on the analysis of tissue expression and stress-responsive expression patterns of rapeseed SRO members and examined their expression profiles under ABA, MeJA and water-deficit drought treatments using qPCR. Transcriptome data analysis and qPCR detection indicated that BnaSROs exhibit multiple stress-responsive expression patterns. BnaSRO1 and BnaSRO11, which are likely to function through interactions with NAC transcription factors, were screened as major drought-regulated members. Our results provide a solid foundation for functional analysis of the role of the SRO gene family in abiotic stress responses, especially drought stress responses, in rapeseed.
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Affiliation(s)
- Huanhuan Jiang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Yuling Zhang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Jia Li
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Rongzi Tang
- Qianxi'nan Academy of Agricultural and Forestry Sciences, Xingyi, Guizhou, China
| | - Fenghao Liang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Rong Tang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Yuyu Zhou
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Chao Zhang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
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32
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Li L, Yu D, Yang J, Zhang F, Zhang D, Lin Z, Zhai M, Wang J, Zhang T, Zhao L. Significant response to pembrolizumab plus lenvatinib in Epstein-Barr-virus-associated intrahepatic cholangiocarcinoma: a case report. Cancer Biol Ther 2024; 25:2338644. [PMID: 38650446 PMCID: PMC11042061 DOI: 10.1080/15384047.2024.2338644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 03/31/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND The prognosis for advanced intrahepatic cholangiocarcinoma (iCCA) is poor, and there remains an urgent need to develop efficient systemic therapy. The efficacy of Pembrolizumab immunotherapy combined with lenvatinibin in iCCA is still unclear. The role of Epstein-Barr-virus (EBV) as a biomarker in iCCA for response to immunotherapy needs further exploration. CASE PRESENTATION We report a case of a 60-year-old female with EBV-associated advanced iCCA (EBVaiCCA) who progressed after first-line therapy. She accomplished an available response to the combination therapy of pembrolizumab with lenvatinib, with overall survival of 20 months. CONCLUSIONS As far as we know, this is the first case report about the application of Pembrolizumab with lenvatinib for EBVaiCCA patients. This case indicates that the combination of immunotherapy and antiangiogenic therapy provides a glimmer of hope for advanced EBVaiCCA patients.
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Affiliation(s)
- Lisha Li
- Cancer Center, Institute of Radiation Oncology, Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dandan Yu
- Cancer Center, Institute of Radiation Oncology, Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jinru Yang
- Cancer Center, Institute of Radiation Oncology, Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fangyuan Zhang
- Cancer Center, Institute of Radiation Oncology, Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dejun Zhang
- Cancer Center, Institute of Radiation Oncology, Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhenyu Lin
- Cancer Center, Institute of Radiation Oncology, Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Menglan Zhai
- Cancer Center, Institute of Radiation Oncology, Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Wang
- Cancer Center, Institute of Radiation Oncology, Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Zhang
- Cancer Center, Institute of Radiation Oncology, Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lei Zhao
- Cancer Center, Institute of Radiation Oncology, Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Sadikiel Mmbando G. The Adoption of Genetically Modified Crops in Africa: the Public's Current Perception, the Regulatory Obstacles, and Ethical Challenges. GM CROPS & FOOD 2024; 15:1-15. [PMID: 38651587 PMCID: PMC11042066 DOI: 10.1080/21645698.2024.2345401] [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: 02/07/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
Genetically modified (GM) crops are the most important agricultural commodities that can improve the yield of African smallholder farmers. The intricate circumstances surrounding the introduction of GM agriculture in Africa, however, underscore the importance of comprehending the moral conundrums, regulatory environments, and public sentiment that exist today. This review examines the current situation surrounding the use of GM crops in Africa, focusing on moral conundrums, regulatory frameworks, and public opinion. Only eleven of the fifty-four African countries currently cultivate GM crops due to the wide range of opinions resulting from the disparities in cultural, socioeconomic, and environmental factors. This review proposed that addressing public concerns, harmonizing regulations, and upholding ethical standards will improve the adoption of GM crops in Africa. This study offers ways to enhance the acceptability of GM crops for boosting nutrition and food security globally.
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Affiliation(s)
- Gideon Sadikiel Mmbando
- Department of Biology, College of Natural and Mathematical Sciences, University of Dodoma, Dodoma, Tanzania
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Li M, Liao L, Huang W, Feng H, Wang W, Huang N, Zhao Z, Shi Y, Ye J, Gu K. Patients with advanced cancer were treated with immune checkpoint inhibitors and injected with COVID-19 vaccine to improve their prognosis without increasing pancreatic related adverse events. Hum Vaccin Immunother 2024; 20:2358575. [PMID: 38836382 PMCID: PMC11155700 DOI: 10.1080/21645515.2024.2358575] [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: 03/13/2024] [Accepted: 05/19/2024] [Indexed: 06/06/2024] Open
Abstract
To investigate immune checkpoint inhibitors (ICIs) induced pancreatic injury (ICIPI), the prognostic effect of COVID-19 vaccine on cancer patients, and whether COVID-19 vaccine increases the incidence of ICIPI. We conducted a retrospective study of 256 stage IV cancer patients treated with ICIs at The First Affiliated Hospital of Anhui Medical University from January 2020 to November 2022. Data collected included pancreatic enzyme levels, treatment outcomes, and vaccination status. Statistical significance was determined using the χ2 test and Kaplan-Meier method (p < .05). Compared to the control group, the vaccinated group (p < .0001) and the group with elevated pancreatic enzyme levels (p = .044) demonstrated higher disease control rates, indicating a direct benefit of vaccination and enzyme monitoring on treatment outcomes. Additionally, vaccinated patients demonstrated longer overall survival versus unvaccinated patients (23.9 months [95% CI, 22.3-25.5] vs 23.6 months [95% CI, 21.1-26.2], HR = 0.45 [95% CI, 0.24-0.86], p = .015) and progression-free survival (17.2 months [95% CI, 14.3-20.1] vs 13.7 months [95% CI, 11.3-16.1], HR = 0.54 [95% CI, 0.36-0.82], p = .004). Importantly, the analysis revealed no significant association between vaccination and pancreatic injury (p = .46). Monitoring pancreatic enzymes can effectively evaluate the therapeutic impact in patients using ICIs. Patients vaccinated against COVID-19 experience better immunotherapy outcomes without an increased risk of ICIPI.
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Affiliation(s)
- Min Li
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lingling Liao
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Wei Huang
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Hui Feng
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Wanqing Wang
- Department of Medical Imaging, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Nana Huang
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhiyan Zhao
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yu Shi
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jinglu Ye
- Department of Endocrinology, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Kangsheng Gu
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
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35
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Grieve LM, Rani A, ZeRuth GT. Downregulation of Glis3 in INS1 cells exposed to chronically elevated glucose contributes to glucotoxicity-associated β cell dysfunction. Islets 2024; 16:2344622. [PMID: 38652652 PMCID: PMC11042057 DOI: 10.1080/19382014.2024.2344622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/15/2024] [Indexed: 04/25/2024] Open
Abstract
Chronically elevated levels of glucose are deleterious to pancreatic β cells and contribute to β cell dysfunction, which is characterized by decreased insulin production and a loss of β cell identity. The Krüppel-like transcription factor, Glis3 has previously been shown to positively regulate insulin transcription and mutations within the Glis3 locus have been associated with the development of several pathologies including type 2 diabetes mellitus. In this report, we show that Glis3 is significantly downregulated at the transcriptional level in INS1 832/13 cells within hours of being subjected to high glucose concentrations and that diminished expression of Glis3 is at least partly attributable to increased oxidative stress. CRISPR/Cas9-mediated knockdown of Glis3 indicated that the transcription factor was required to maintain normal levels of both insulin and MafA expression and reduced Glis3 expression was concomitant with an upregulation of β cell disallowed genes. We provide evidence that Glis3 acts similarly to a pioneer factor at the insulin promoter where it permissively remodels the chromatin to allow access to a transcriptional regulatory complex including Pdx1 and MafA. Finally, evidence is presented that Glis3 can positively regulate MafA transcription through its pancreas-specific promoter and that MafA reciprocally regulates Glis3 expression. Collectively, these results suggest that decreased Glis3 expression in β cells exposed to chronic hyperglycemia may contribute significantly to reduced insulin transcription and a loss of β cell identity.
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Affiliation(s)
- LilyAnne M. Grieve
- Department of Biological Sciences, Murray State University, Murray, KY, USA
| | - Abhya Rani
- Department of Biological Sciences, Murray State University, Murray, KY, USA
| | - Gary T. ZeRuth
- Department of Biological Sciences, Murray State University, Murray, KY, USA
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36
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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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37
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Ma D, Liu S, Liu K, Kong L, Xiao L, Xin Q, Jiang C, Wu J. MDFI promotes the proliferation and tolerance to chemotherapy of colorectal cancer cells by binding ITGB4/LAMB3 to activate the AKT signaling pathway. Cancer Biol Ther 2024; 25:2314324. [PMID: 38375821 PMCID: PMC10880501 DOI: 10.1080/15384047.2024.2314324] [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: 09/21/2023] [Accepted: 01/31/2024] [Indexed: 02/21/2024] Open
Abstract
Colorectal cancer (CRC) is one of the most lethal cancers. Single-cell RNA sequencing (scRNA-seq) and protein-protein interactions (PPIs) have enabled the systematic study of CRC. In our research, the activation of the AKT pathway in CRC was analyzed by KEGG using single-cell sequencing data from the GSE144735 dataset. The correlation and PPIs of MDFI and ITGB4/LAMB3 were examined. The results were verified in the TCGA and CCLE and further tested by coimmunoprecipitation experiments. The effect of MDFI on the AKT pathway via ITGB4/LAMB3 was validated by knockdown and lentiviral overexpression experiments. The effect of MDFI on oxaliplatin/fluorouracil sensitivity was probed by colony formation assay and CCK8 assay. We discovered that MDFI was positively associated with ITGB4/LAMB3. In addition, MDFI was negatively associated with oxaliplatin/fluorouracil sensitivity. MDFI upregulated the AKT pathway by directly interacting with LAMB3 and ITGB4 in CRC cells, and enhanced the proliferation of CRC cells via the AKT pathway. Finally, MDFI reduced the sensitivity of CRC cells to oxaliplatin and fluorouracil. In conclusion, MDFI promotes the proliferation and tolerance to chemotherapy of colorectal cancer cells, partially through the activation of the AKT signaling pathway by the binding to ITGB4/LAMB3. Our findings provide a possible molecular target for CRC therapy.
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Affiliation(s)
- Ding Ma
- State Key Laboratory of Pharmaceutical Biotechnology, National Institute of Healthcare Data Science at Nanjing University, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, Jiangsu, China
- Department of Gastroenterology, Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shuwen Liu
- State Key Laboratory of Pharmaceutical Biotechnology, National Institute of Healthcare Data Science at Nanjing University, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, Jiangsu, China
| | - Kua Liu
- State Key Laboratory of Pharmaceutical Biotechnology, National Institute of Healthcare Data Science at Nanjing University, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, Jiangsu, China
| | - Lingkai Kong
- State Key Laboratory of Pharmaceutical Biotechnology, National Institute of Healthcare Data Science at Nanjing University, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, Jiangsu, China
| | - Lingjun Xiao
- State Key Laboratory of Pharmaceutical Biotechnology, National Institute of Healthcare Data Science at Nanjing University, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, Jiangsu, China
| | - Qilei Xin
- Jinan Microecological Biomedicine Shandong Laboratory, Shounuo City Light West Block, Jinan City, Shandong Province, China
| | - Chunping Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, National Institute of Healthcare Data Science at Nanjing University, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, Jiangsu, China
- Jinan Microecological Biomedicine Shandong Laboratory, Shounuo City Light West Block, Jinan City, Shandong Province, China
| | - Junhua Wu
- State Key Laboratory of Pharmaceutical Biotechnology, National Institute of Healthcare Data Science at Nanjing University, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, Jiangsu, China
- Jinan Microecological Biomedicine Shandong Laboratory, Shounuo City Light West Block, Jinan City, Shandong Province, China
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38
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Guo X, Song J, Liu M, Ou X, Guo Y. The interplay between the tumor microenvironment and tumor-derived small extracellular vesicles in cancer development and therapeutic response. Cancer Biol Ther 2024; 25:2356831. [PMID: 38767879 PMCID: PMC11110713 DOI: 10.1080/15384047.2024.2356831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 05/14/2024] [Indexed: 05/22/2024] Open
Abstract
The tumor microenvironment (TME) plays an essential role in tumor cell survival by profoundly influencing their proliferation, metastasis, immune evasion, and resistance to treatment. Extracellular vesicles (EVs) are small particles released by all cell types and often reflect the state of their parental cells and modulate other cells' functions through the various cargo they transport. Tumor-derived small EVs (TDSEVs) can transport specific proteins, nucleic acids and lipids tailored to propagate tumor signals and establish a favorable TME. Thus, the TME's biological characteristics can affect TDSEV heterogeneity, and this interplay can amplify tumor growth, dissemination, and resistance to therapy. This review discusses the interplay between TME and TDSEVs based on their biological characteristics and summarizes strategies for targeting cancer cells. Additionally, it reviews the current issues and challenges in this field to offer fresh insights into comprehending tumor development mechanisms and exploring innovative clinical applications.
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Affiliation(s)
- Xuanyu Guo
- The Affiliated Hospital, Southwest Medical University, Luzhou, PR China
| | - Jiajun Song
- Department of Clinical Laboratory Medicine, the Affiliated Hospital, Southwest Medical University, Luzhou, PR China
| | - Miao Liu
- Nanobiosensing and Microfluidic Point-of-Care Testing, Key Laboratory of Luzhou, Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, PR China
| | - Xinyi Ou
- Nanobiosensing and Microfluidic Point-of-Care Testing, Key Laboratory of Luzhou, Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, PR China
| | - Yongcan Guo
- Nanobiosensing and Microfluidic Point-of-Care Testing, Key Laboratory of Luzhou, Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, PR China
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39
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Wang Y, Zou H, Ji W, Huang M, You B, Sun N, Qiao Y, Liu P, Xu L, Zhang X, Cai M, Kuang Y, Fu S, Sun W, Jia X, Wu J. Repression of the SUMO-conjugating enzyme UBC9 is associated with lowered double minutes and reduced tumor progression. Cancer Biol Ther 2024; 25:2323768. [PMID: 38465861 PMCID: PMC10936631 DOI: 10.1080/15384047.2024.2323768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/22/2024] [Indexed: 03/12/2024] Open
Abstract
Double minutes (DMs), extrachromosomal gene fragments found within certain tumors, have been noted to carry onco- and drug resistance genes contributing to tumor pathogenesis and progression. After screening for SUMO-related molecule expression within various tumor sample and cell line databases, we found that SUMO-conjugating enzyme UBC9 has been associated with genome instability and tumor cell DM counts, which was confirmed both in vitro and in vivo. Karyotyping determined DM counts post-UBC9 knockdown or SUMOylation inhibitor 2-D08, while RT-qPCR and Western blot were used to measure DM-carried gene expression in vitro. In vivo, fluorescence in situ hybridization (FISH) identified micronucleus (MN) expulsion. Western blot and immunofluorescence staining were then used to determine DNA damage extent, and a reporter plasmid system was constructed to detect changes in homologous recombination (HR) and non-homologous end joining (NHEJ) pathways. Our research has shown that UBC9 inhibition is able to attenuate DM formation and lower DM-carried gene expression, in turn reducing tumor growth and malignant phenotype, via MN efflux of DMs and lowering NHEJ activity to increase DNA damage. These findings thus reveal a relationship between heightened UBC9 activity, increased DM counts, and tumor progression, providing a potential approach for targeted therapies, via UBC9 inhibition.
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Affiliation(s)
- Yusi Wang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Hongyan Zou
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Wei Ji
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Min Huang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Benhui You
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Nan Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Yuandong Qiao
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Peng Liu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Lidan Xu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Xuelong Zhang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Mengdi Cai
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Ye Kuang
- Department of Gynecology and Obstetrics, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Songbin Fu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Wenjing Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Xueyuan Jia
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Jie Wu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
- Future Medical Laboratory, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
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40
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Colwill M, Baillie S, Pollok R, Poullis A. Biobanks and biomarkers: Their current and future role in biomedical research. World J Methodol 2024; 14:91387. [DOI: 10.5662/wjm.v14.i4.91387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 05/27/2024] [Accepted: 06/11/2024] [Indexed: 07/26/2024] Open
Abstract
The importance and utility of biobanks has increased exponentially since their inception and creation. Initially used as part of translational research, they now contribute over 40% of data for all cancer research papers in the United States of America and play a crucial role in all aspects of healthcare. Multiple classification systems exist but a simplified approach is to either classify as population-based or disease-oriented entities. Whilst historically publicly funded institutions, there has been a significant increase in industry funded entities across the world which has changed the dynamic of biobanks offering new possibilities but also new challenges. Biobanks face legal questions over data sharing and intellectual property as well as ethical and sustainability questions particularly as the world attempts to move to a low-carbon economy. International collaboration is required to address some of these challenges but this in itself is fraught with complexity and difficulty. This review will examine the current utility of biobanks in the modern healthcare setting as well as the current and future challenges these vital institutions face.
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Affiliation(s)
- Michael Colwill
- Department of Gastroenterology, St George's University Hospital NHS Foundation Trust, London SW17 0QT, United Kingdom
| | - Samantha Baillie
- Department of Gastroenterology, St George's University Hospital NHS Foundation Trust, London SW17 0QT, United Kingdom
| | - Richard Pollok
- Department of Gastroenterology, St George's University Hospital NHS Foundation Trust, London SW17 0QT, United Kingdom
| | - Andrew Poullis
- Department of Gastroenterology, St George's University Hospital NHS Foundation Trust, London SW17 0QT, United Kingdom
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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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Yao M, Zhang L, Teng X, Lei Y, Xing X, Ren T, Pan Y, Zhang L, Li Z, Lin J, Zheng Y, Xing L, Zhou J, Wu C. Transcriptomic profiling of Dip2a in the neural differentiation of mouse embryonic stem cells. Comput Struct Biotechnol J 2024; 23:700-710. [PMID: 38292475 PMCID: PMC10825174 DOI: 10.1016/j.csbj.2023.12.032] [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: 10/06/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 02/01/2024] Open
Abstract
Introduction The disconnected-interacting protein 2 homolog A (DIP2A), a member of disconnected-interacting 2 protein family, has been shown to be involved in human nervous system-related mental illness. This protein is highly expressed in the nervous system of mouse. Mutation of mouse DIP2A causes defects in spine morphology and synaptic transmission, autism-like behaviors, and defective social novelty [5], [27], indicating that DIP2A is critical to the maintenance of neural development. However, the role of DIP2A in neural differentiation has yet to be investigated. Objective To determine the role of DIP2A in neural differentiation, a neural differentiation model was established using mouse embryonic stem cells (mESCs) and studied by using gene-knockout technology and RNA-sequencing-based transcriptome analysis. Results We found that DIP2A is not required for mESCs pluripotency maintenance, but loss of DIP2A causes the neural differentiation abnormalities in both N2B27 and KSR medium. Functional knockout of Dip2a gene also decreased proliferation of mESCs by perturbation of the cell cycle and profoundly inhibited the expression of a large number of neural development-associated genes which mainly enriched in spinal cord development and postsynapse assembly. Conclusions The results of this report demonstrate that DIP2A plays an essential role in regulating differentiation of mESCs towards the neural fate.
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Affiliation(s)
- Mingze Yao
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Lei Zhang
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
- Center of Reproductive Medicine, Children's Hospital of Shanxi and Women Health Center of Shanxi, Taiyuan 030006, China
| | - Xiaojuan Teng
- Dermatology Hospital, Southern Medical University, Guangzhou 510000, China
| | - Yu Lei
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Xiaoyu Xing
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Tinglin Ren
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Yuanqing Pan
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Liwen Zhang
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Zhengfeng Li
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510000, China
| | - Jingxia Lin
- Dermatology Hospital, Southern Medical University, Guangzhou 510000, China
| | - Yaowu Zheng
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Li Xing
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Jiajian Zhou
- Dermatology Hospital, Southern Medical University, Guangzhou 510000, China
| | - Changxin Wu
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
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Wang C, Chen Z, Copenhaver GP, Wang Y. Heterochromatin in plant meiosis. Nucleus 2024; 15:2328719. [PMID: 38488152 PMCID: PMC10950279 DOI: 10.1080/19491034.2024.2328719] [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: 09/11/2023] [Accepted: 03/05/2024] [Indexed: 03/19/2024] Open
Abstract
Heterochromatin is an organizational property of eukaryotic chromosomes, characterized by extensive DNA and histone modifications, that is associated with the silencing of transposable elements and repetitive sequences. Maintaining heterochromatin is crucial for ensuring genomic integrity and stability during the cell cycle. During meiosis, heterochromatin is important for homologous chromosome synapsis, recombination, and segregation, but our understanding of meiotic heterochromatin formation and condensation is limited. In this review, we focus on the dynamics and features of heterochromatin and how it condenses during meiosis in plants. We also discuss how meiotic heterochromatin influences the interaction and recombination of homologous chromosomes during prophase I.
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Affiliation(s)
- Cong Wang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Zhiyu Chen
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Gregory P. Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Yingxiang Wang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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Cairns CA, Xiao L, Wang JY. Posttranscriptional Regulation of Intestinal Mucosal Growth and Adaptation by Noncoding RNAs in Critical Surgical Disorders. J INVEST SURG 2024; 37:2308809. [PMID: 38323630 PMCID: PMC11027105 DOI: 10.1080/08941939.2024.2308809] [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: 06/03/2023] [Accepted: 01/12/2024] [Indexed: 02/08/2024]
Abstract
The human intestinal epithelium has an impressive ability to respond to insults and its homeostasis is maintained by well-regulated mechanisms under various pathophysiological conditions. Nonetheless, acute injury and inhibited regeneration of the intestinal epithelium occur commonly in critically ill surgical patients, leading to the translocation of luminal toxic substances and bacteria to the bloodstream. Effective therapies for the preservation of intestinal epithelial integrity and for the prevention of mucosal hemorrhage and gut barrier dysfunction are limited, primarily because of a poor understanding of the mechanisms underlying mucosal disruption. Noncoding RNAs (ncRNAs), which include microRNAs (miRNAs), long ncRNAs (lncRNAs), circular RNAs (circRNAs), and small vault RNAs (vtRNAs), modulate a wide array of biological functions and have been identified as orchestrators of intestinal epithelial homeostasis. Here, we feature the roles of many important ncRNAs in controlling intestinal mucosal growth, barrier function, and repair after injury-particularly in the context of postoperative recovery from bowel surgery. We review recent literature surrounding the relationships between lncRNAs, microRNAs, and RNA-binding proteins and how their interactions impact cell survival, proliferation, migration, and cell-to-cell interactions in the intestinal epithelium. With advancing knowledge of ncRNA biology and growing recognition of the importance of ncRNAs in maintaining the intestinal epithelial integrity, ncRNAs provide novel therapeutic targets for treatments to preserve the gut epithelium in individuals suffering from critical surgical disorders.
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Affiliation(s)
- Cassandra A. Cairns
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Lan Xiao
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Jian-Ying Wang
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland 21201
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland 21201
- Baltimore Veterans Affairs Medical Center, Baltimore, Maryland 21201
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Xiao CK, Ren Y, Chen Q, Yang Y, Tang L, Xu L, Ren Z. H4K20me3, H3K4me2 and H3K9me2 mediate the effect of ER on prognosis in breast cancer. Epigenetics 2024; 19:2343593. [PMID: 38643489 PMCID: PMC11037280 DOI: 10.1080/15592294.2024.2343593] [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: 09/11/2023] [Accepted: 04/09/2024] [Indexed: 04/23/2024] Open
Abstract
Previous studies have indicated that histone methylations act as mediators in the relationship between oestrogen receptor (ER) and breast cancer prognosis, yet the mediating role has never been assessed. Therefore, we investigated seven histone methylations (H3K4me2, H3K4me3, H3K9me1, H3K9me2, H3K9me3, H3K27me3 and H4K20me3) to determine whether they mediate the prognostic impact of ER on breast cancer. Tissue microarrays were constructed from 1045 primary invasive breast tumours, and the expressions of histone methylations were examined by immunohistochemistry. Multifactorial logistic regression was used to analyse the associations between ER and histone methylations. Cox proportional hazard model was performed to assess the relationship between histone methylations and breast cancer prognosis. The mediation effects of histone methylations were evaluated by model-based causal mediation analysis. High expressions of H3K9me1, H3K9me2, H3K4me2, H3K27me3, H4K20me3 were associated with ER positivity, while high expression of H3K9me3 was associated ER negativity. Higher H3K9me2, H3K4me2 and H4K20me3 levels were associated with better prognosis. The association between ER and breast cancer prognosis was most strongly mediated by H4K20me3 (29.07% for OS; 22.42% for PFS), followed by H3K4me2 (11.5% for OS; 10.82% for PFS) and least by H3K9me2 (9.35% for OS; 7.34% for PFS). H4K20me3, H3K4me2 and H3K9me2 mediated the relationship between ER and breast cancer prognosis, which would help to further elucidate the impact of ER on breast cancer prognosis from an epigenetic perspective and provide new ideas for breast cancer treatment.
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Affiliation(s)
- Cheng-Kun Xiao
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yuexiang Ren
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Qianxin Chen
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yuanzhong Yang
- The Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Luying Tang
- The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Lin Xu
- School of Public Health, Sun Yat-sen University, Guangzhou, China
- School of Public Health, the University of Hong Kong, Hong Kong, China
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Zefang Ren
- School of Public Health, Sun Yat-sen University, Guangzhou, China
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Jaeger M, Dietschmann A, Austermeier S, Dinçer S, Porschitz P, Vornholz L, Maas RJ, Sprenkeler EG, Ruland J, Wirtz S, Azam T, Joosten LA, Hube B, Netea MG, Dinarello CA, Gresnigt MS. Alpha1-antitrypsin impacts innate host-pathogen interactions with Candida albicans by stimulating fungal filamentation. Virulence 2024; 15:2333367. [PMID: 38515333 PMCID: PMC11008552 DOI: 10.1080/21505594.2024.2333367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
Our immune system possesses sophisticated mechanisms to cope with invading microorganisms, while pathogens evolve strategies to deal with threats imposed by host immunity. Human plasma protein α1-antitrypsin (AAT) exhibits pleiotropic immune-modulating properties by both preventing immunopathology and improving antimicrobial host defence. Genetic associations suggested a role for AAT in candidemia, the most frequent fungal blood stream infection in intensive care units, yet little is known about how AAT influences interactions between Candida albicans and the immune system. Here, we show that AAT differentially impacts fungal killing by innate phagocytes. We observed that AAT induces fungal transcriptional reprogramming, associated with cell wall remodelling and downregulation of filamentation repressors. At low concentrations, the cell-wall remodelling induced by AAT increased immunogenic β-glucan exposure and consequently improved fungal clearance by monocytes. Contrastingly, higher AAT concentrations led to excessive C. albicans filamentation and thus promoted fungal immune escape from monocytes and macrophages. This underscores that fungal adaptations to the host protein AAT can differentially define the outcome of encounters with innate immune cells, either contributing to improved immune recognition or fungal immune escape.
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Affiliation(s)
- Martin Jaeger
- Department of Medicine, University of Colorado Denver, Aurora, USA
- Department of Internal Medicine, Radboud University Medical Center and Radboud Center for Infectious diseases (RCI), Nijmegen, the Netherlands
| | - Axel Dietschmann
- Junior Research Group Adaptive Pathogenicity Strategies, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Sophie Austermeier
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Sude Dinçer
- Junior Research Group Adaptive Pathogenicity Strategies, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Pauline Porschitz
- Junior Research Group Adaptive Pathogenicity Strategies, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Larsen Vornholz
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine and Health, Center for Translational Cancer Research (TranslaTUM), Munich, Germany
| | - Ralph J.A. Maas
- Department of Medicine, University of Colorado Denver, Aurora, USA
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Evelien G.G. Sprenkeler
- Department of Internal Medicine, Radboud University Medical Center and Radboud Center for Infectious diseases (RCI), Nijmegen, the Netherlands
| | - Jürgen Ruland
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine and Health, Center for Translational Cancer Research (TranslaTUM), Munich, Germany
- German Cancer Consortium (DKTK), partner site Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, Germany
| | - Stefan Wirtz
- Medizinische Klinik 1, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Tania Azam
- Department of Medicine, University of Colorado Denver, Aurora, USA
| | - Leo A.B. Joosten
- Department of Internal Medicine, Radboud University Medical Center and Radboud Center for Infectious diseases (RCI), Nijmegen, the Netherlands
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
- Institute of Microbiology, Friedrich-Schiller-University, Jena, Germany
| | - Mihai G. Netea
- Department of Internal Medicine, Radboud University Medical Center and Radboud Center for Infectious diseases (RCI), Nijmegen, the Netherlands
| | - Charles A. Dinarello
- Department of Medicine, University of Colorado Denver, Aurora, USA
- Department of Internal Medicine, Radboud University Medical Center and Radboud Center for Infectious diseases (RCI), Nijmegen, the Netherlands
| | - Mark S. Gresnigt
- Department of Medicine, University of Colorado Denver, Aurora, USA
- Junior Research Group Adaptive Pathogenicity Strategies, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
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Li G, Hu Z, Luo X, Liu J, Wu J, Peng W, Zhu X. Identification of cancer driver genes based on hierarchical weak consensus model. Health Inf Sci Syst 2024; 12:21. [PMID: 38464463 PMCID: PMC10917728 DOI: 10.1007/s13755-024-00279-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 01/31/2024] [Indexed: 03/12/2024] Open
Abstract
Cancer is a complex gene mutation disease that derives from the accumulation of mutations during somatic cell evolution. With the advent of high-throughput technology, a large amount of omics data has been generated, and how to find cancer-related driver genes from a large number of omics data is a challenge. In the early stage, the researchers developed many frequency-based driver genes identification methods, but they could not identify driver genes with low mutation rates well. Afterwards, researchers developed network-based methods by fusing multi-omics data, but they rarely considered the connection among features. In this paper, after analyzing a large number of methods for integrating multi-omics data, a hierarchical weak consensus model for fusing multiple features is proposed according to the connection among features. By analyzing the connection between PPI network and co-mutation hypergraph network, this paper firstly proposes a new topological feature, called co-mutation clustering coefficient (CMCC). Then, a hierarchical weak consensus model is used to integrate CMCC, mRNA and miRNA differential expression scores, and a new driver genes identification method HWC is proposed. In this paper, the HWC method and current 7 state-of-the-art methods are compared on three types of cancers. The comparison results show that HWC has the best identification performance in statistical evaluation index, functional consistency and the partial area under ROC curve. Supplementary Information The online version contains supplementary material available at 10.1007/s13755-024-00279-6.
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Affiliation(s)
- Gaoshi Li
- Key Lab of Education Blockchain and Intelligent Technology, Ministry of Education, Guangxi Normal University, Guilin, 541004 China
- Guangxi Key Lab of Multi-Source Information Mining & Security, Guangxi Normal University, Guilin, 541004 Guangxi China
- College of Computer Science and Engineering, Guangxi Normal University, Guilin, 541004 Guangxi China
| | - Zhipeng Hu
- Key Lab of Education Blockchain and Intelligent Technology, Ministry of Education, Guangxi Normal University, Guilin, 541004 China
- Guangxi Key Lab of Multi-Source Information Mining & Security, Guangxi Normal University, Guilin, 541004 Guangxi China
- College of Computer Science and Engineering, Guangxi Normal University, Guilin, 541004 Guangxi China
| | - Xinlong Luo
- Key Lab of Education Blockchain and Intelligent Technology, Ministry of Education, Guangxi Normal University, Guilin, 541004 China
- Guangxi Key Lab of Multi-Source Information Mining & Security, Guangxi Normal University, Guilin, 541004 Guangxi China
- College of Computer Science and Engineering, Guangxi Normal University, Guilin, 541004 Guangxi China
| | - Jiafei Liu
- Key Lab of Education Blockchain and Intelligent Technology, Ministry of Education, Guangxi Normal University, Guilin, 541004 China
- Guangxi Key Lab of Multi-Source Information Mining & Security, Guangxi Normal University, Guilin, 541004 Guangxi China
- College of Computer Science and Engineering, Guangxi Normal University, Guilin, 541004 Guangxi China
| | - Jingli Wu
- Key Lab of Education Blockchain and Intelligent Technology, Ministry of Education, Guangxi Normal University, Guilin, 541004 China
- Guangxi Key Lab of Multi-Source Information Mining & Security, Guangxi Normal University, Guilin, 541004 Guangxi China
- College of Computer Science and Engineering, Guangxi Normal University, Guilin, 541004 Guangxi China
| | - Wei Peng
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, 650500 Yunnan China
| | - Xiaoshu Zhu
- Key Lab of Education Blockchain and Intelligent Technology, Ministry of Education, Guangxi Normal University, Guilin, 541004 China
- Guangxi Key Lab of Multi-Source Information Mining & Security, Guangxi Normal University, Guilin, 541004 Guangxi China
- College of Computer Science and Engineering, Guangxi Normal University, Guilin, 541004 Guangxi China
- School of Computer and Information Security & School of Software Engineering, Guilin University of Electronic Science and Technology, Guilin, China
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Zeng W, Zheng L, Li Y, Yang J, Mao T, Zhang J, Liu Y, Ning J, Zhang T, Huang H, Chen X, Lu F. Engineered extracellular vesicles for delivering functional Cas9/gRNA to eliminate hepatitis B virus cccDNA and integration. Emerg Microbes Infect 2024; 13:2284286. [PMID: 37982370 PMCID: PMC10763861 DOI: 10.1080/22221751.2023.2284286] [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: 05/17/2023] [Accepted: 11/13/2023] [Indexed: 11/21/2023]
Abstract
The persistence of HBV covalently closed circular DNA (cccDNA) and HBV integration into the host genome in infected hepatocytes pose significant challenges to the cure of chronic HBV infection. Although CRISPR/Cas9-mediated genome editing shows promise for targeted clearance of viral genomes, a safe and efficient delivery method is currently lacking. Here, we developed a novel approach by combining light-induced heterodimerization and protein acylation to enhance the loading efficiency of Cas9 protein into extracellular vesicles (EVs). Moreover, vesicular stomatitis virus-glycoprotein (VSV-G) was incorporated onto the EVs membrane, significantly facilitating the endosomal escape of Cas9 protein and increasing its gene editing activity in recipient cells. Our results demonstrated that engineered EVs containing Cas9/gRNA and VSV-G can effectively reduce viral antigens and cccDNA levels in the HBV-replicating and infected cell models. Notably, we also confirmed the antiviral activity and high safety of the engineered EVs in the HBV-replicating mouse model generated by hydrodynamic injection and the HBV transgenic mouse model. In conclusion, engineered EVs could successfully mediate functional CRISPR/Cas9 delivery both in vitro and in vivo, leading to the clearance of episomal cccDNA and integrated viral DNA fragments, and providing a novel therapeutic approach for curing chronic HBV infection.
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Affiliation(s)
- Wanjia Zeng
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People’s Republic of China
| | - Liwei Zheng
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People’s Republic of China
| | - Yukun Li
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People’s Republic of China
| | - Jing Yang
- School of Medicine, Shihezi University, Shihezi, People’s Republic of China
| | - Tianhao Mao
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People’s Republic of China
| | - Jing Zhang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People’s Republic of China
| | - Yanna Liu
- Department of Gastroenterology and Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Jing Ning
- Department of Gastroenterology, Beijing Key Laboratory for Helicobacter Pylori Infection and Upper Gastrointestinal Diseases, Peking University Third Hospital, Beijing, People’s Republic of China
| | - Ting Zhang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People’s Republic of China
| | - Hongxin Huang
- Department of Pathogen Biology and Biosecurity, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Xiangmei Chen
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People’s Republic of China
| | - Fengmin Lu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People’s Republic of China
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Moeckel C, Mareboina M, Konnaris MA, Chan CS, Mouratidis I, Montgomery A, Chantzi N, Pavlopoulos GA, Georgakopoulos-Soares I. A survey of k-mer methods and applications in bioinformatics. Comput Struct Biotechnol J 2024; 23:2289-2303. [PMID: 38840832 PMCID: PMC11152613 DOI: 10.1016/j.csbj.2024.05.025] [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: 03/13/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 06/07/2024] Open
Abstract
The rapid progression of genomics and proteomics has been driven by the advent of advanced sequencing technologies, large, diverse, and readily available omics datasets, and the evolution of computational data processing capabilities. The vast amount of data generated by these advancements necessitates efficient algorithms to extract meaningful information. K-mers serve as a valuable tool when working with large sequencing datasets, offering several advantages in computational speed and memory efficiency and carrying the potential for intrinsic biological functionality. This review provides an overview of the methods, applications, and significance of k-mers in genomic and proteomic data analyses, as well as the utility of absent sequences, including nullomers and nullpeptides, in disease detection, vaccine development, therapeutics, and forensic science. Therefore, the review highlights the pivotal role of k-mers in addressing current genomic and proteomic problems and underscores their potential for future breakthroughs in research.
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Affiliation(s)
- Camille Moeckel
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Manvita Mareboina
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Maxwell A. Konnaris
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Candace S.Y. Chan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Ioannis Mouratidis
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Huck Institute of the Life Sciences, Penn State University, University Park, Pennsylvania, USA
| | - Austin Montgomery
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Nikol Chantzi
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | | | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Huck Institute of the Life Sciences, Penn State University, University Park, Pennsylvania, USA
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Xue Y, Xia Y, Cheng D, Shi T, Mei P, Hong S. Association between genetically proxied PPARG activation and psoriasis vulgaris: a Mendelian randomization study. J DERMATOL TREAT 2024; 35:2381763. [PMID: 39034037 DOI: 10.1080/09546634.2024.2381763] [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: 05/24/2024] [Accepted: 07/03/2024] [Indexed: 07/23/2024]
Abstract
BACKGROUND Psoriasis is a common autoimmune disease in clinical practice, and previous observational studies have suggested that PPARG agonists such as Pioglitazone may be potential therapeutic agents. However, due to interference from various confounding factors, different observational studies have not reached a unified conclusion. We aim to evaluate the potential use of PPARG agonists for treating psoriasis from a new perspective through drug-targeted Mendelian randomization (MR) analysis. MATERIALS AND METHODS This study includes data on 8,876 individuals for acute myocardial infarction from GWAS, and LDL cholesterol data from 343,621 Europeans. FinnGen contributed psoriasis vulgaris data for 403,972 individuals. The DrugBank10 databases function to identify genes encoding protein products targeted by active constituents of lipid-modifying targets. A two-sample MR analysis and summary-data-based MR (SMR) analysis estimated the associations between expressions of drug target genes and symptoms of psoriasis vulgaris. A multivariable MR study was further conducted to examine if the observed association was direct association. RESULTS SMR analysis revealed that enhanced PPARG gene expression in the blood (equivalent to a one standard deviation increase) was a protective factor for psoriasis vulgaris (beta = -0.2017, se = 0.0723, p = 0.0053). Besides, there exists an MR association between LDL mediated by PPARG and psoriasis vulgaris outcomes (beta = -3.9169, se = 0.5676, p = 5.17E-12). These results indicate that PPARG is a therapeutic target for psoriasis, suggesting that psoriasis may be a potential indication for PPARG agonists. CONCLUSION This study confirms that therapeutic activation of PPARG helps suppress the development of psoriasis. Psoriasis may be a new indication for PPARG agonists, such as Pioglitazone. In the future, new anti-psoriatic drugs could be developed targeting PPARG.
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Affiliation(s)
- Yan Xue
- Department of Dermatology, First Affiliated Hospital of Naval Military Medical University, Shanghai, China
| | - Yuning Xia
- First Clinical Medical College (First Affiliated Hospital), Anhui Medical University, Hefei, China
| | - Donghao Cheng
- First Clinical Medical College (First Affiliated Hospital), Anhui Medical University, Hefei, China
| | - Taiyu Shi
- First Clinical Medical College (First Affiliated Hospital), Anhui Medical University, Hefei, China
| | - Ping Mei
- Department of Radiology, Anqing Municipal Hospital, Anqing, China
| | - Sheng Hong
- Department of Dermatology, First Affiliated Hospital of Naval Military Medical University, Shanghai, China
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