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Mitrofanis J, Stone J, Hamblin MR, Magistretti P, Benabid AL, Jeffery G. A spotlight on dosage and subject selection for effective neuroprotection: exploring the central role of mitochondria. Neural Regen Res 2025; 20:1081-1082. [PMID: 38989941 DOI: 10.4103/nrr.nrr-d-24-00222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/30/2024] [Indexed: 07/12/2024] Open
Affiliation(s)
- John Mitrofanis
- Fonds Clinatec, Université Grenoble Alpes, Grenoble, France (Mitrofanis J, Benabid AL)
- Institute of Ophthalmology, University College London, London, UK (Mitrofanis J, Jeffery G)
| | - Jonathan Stone
- School of Medical Science, University of Sydney, Sydney, Australia (Stone J)
| | - Michael R Hamblin
- Faculty of Health Sciences, University of Johannesburg, Johannesburg, South Africa (Hamblin MR)
| | - Pierre Magistretti
- King Abdullah University of Science and Technology, Thuwal, Saudi Arabia (Magistretti P)
| | - Alim-Louis Benabid
- Fonds Clinatec, Université Grenoble Alpes, Grenoble, France (Mitrofanis J, Benabid AL)
| | - Glen Jeffery
- Institute of Ophthalmology, University College London, London, UK (Mitrofanis J, Jeffery G)
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2
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Pérez-Núñez R, González MF, Avalos AM, Leyton L. Impacts of PI3K/protein kinase B pathway activation in reactive astrocytes: from detrimental effects to protective functions. Neural Regen Res 2025; 20:1031-1041. [PMID: 38845231 DOI: 10.4103/nrr.nrr-d-23-01756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 05/06/2024] [Indexed: 07/12/2024] Open
Abstract
Astrocytes are the most abundant type of glial cell in the central nervous system. Upon injury and inflammation, astrocytes become reactive and undergo morphological and functional changes. Depending on their phenotypic classification as A1 or A2, reactive astrocytes contribute to both neurotoxic and neuroprotective responses, respectively. However, this binary classification does not fully capture the diversity of astrocyte responses observed across different diseases and injuries. Transcriptomic analysis has revealed that reactive astrocytes have a complex landscape of gene expression profiles, which emphasizes the heterogeneous nature of their reactivity. Astrocytes actively participate in regulating central nervous system inflammation by interacting with microglia and other cell types, releasing cytokines, and influencing the immune response. The phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT) signaling pathway is a central player in astrocyte reactivity and impacts various aspects of astrocyte behavior, as evidenced by in silico , in vitro , and in vivo results. In astrocytes, inflammatory cues trigger a cascade of molecular events, where nuclear factor-κB serves as a central mediator of the pro-inflammatory responses. Here, we review the heterogeneity of reactive astrocytes and the molecular mechanisms underlying their activation. We highlight the involvement of various signaling pathways that regulate astrocyte reactivity, including the PI3K/AKT/mammalian target of rapamycin (mTOR), α v β 3 integrin/PI3K/AKT/connexin 43, and Notch/PI3K/AKT pathways. While targeting the inactivation of the PI3K/AKT cellular signaling pathway to control reactive astrocytes and prevent central nervous system damage, evidence suggests that activating this pathway could also yield beneficial outcomes. This dual function of the PI3K/AKT pathway underscores its complexity in astrocyte reactivity and brain function modulation. The review emphasizes the importance of employing astrocyte-exclusive models to understand their functions accurately and these models are essential for clarifying astrocyte behavior. The findings should then be validated using in vivo models to ensure real-life relevance. The review also highlights the significance of PI3K/AKT pathway modulation in preventing central nervous system damage, although further studies are required to fully comprehend its role due to varying factors such as different cell types, astrocyte responses to inflammation, and disease contexts. Specific strategies are clearly necessary to address these variables effectively.
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Affiliation(s)
- Ramón Pérez-Núñez
- Cellular Communication Laboratory, Programa de Biología Celular y Molecular, Center for Studies on Exercise, Metabolism and Cancer (CEMC), Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Advanced Center for Chronic Diseases (ACCDiS), Faculty of Chemical and Pharmaceutical Sciences & Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - María Fernanda González
- Cellular Communication Laboratory, Programa de Biología Celular y Molecular, Center for Studies on Exercise, Metabolism and Cancer (CEMC), Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Advanced Center for Chronic Diseases (ACCDiS), Faculty of Chemical and Pharmaceutical Sciences & Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Ana María Avalos
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago, Chile
| | - Lisette Leyton
- Cellular Communication Laboratory, Programa de Biología Celular y Molecular, Center for Studies on Exercise, Metabolism and Cancer (CEMC), Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Advanced Center for Chronic Diseases (ACCDiS), Faculty of Chemical and Pharmaceutical Sciences & Faculty of Medicine, Universidad de Chile, Santiago, Chile
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3
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Gao M, Wang X, Su S, Feng W, Lai Y, Huang K, Cao D, Wang Q. Meningeal lymphatic vessel crosstalk with central nervous system immune cells in aging and neurodegenerative diseases. Neural Regen Res 2025; 20:763-778. [PMID: 38886941 DOI: 10.4103/nrr.nrr-d-23-01595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 12/22/2023] [Indexed: 06/20/2024] Open
Abstract
Meningeal lymphatic vessels form a relationship between the nervous system and periphery, which is relevant in both health and disease. Meningeal lymphatic vessels not only play a key role in the drainage of brain metabolites but also contribute to antigen delivery and immune cell activation. The advent of novel genomic technologies has enabled rapid progress in the characterization of myeloid and lymphoid cells and their interactions with meningeal lymphatic vessels within the central nervous system. In this review, we provide an overview of the multifaceted roles of meningeal lymphatic vessels within the context of the central nervous system immune network, highlighting recent discoveries on the immunological niche provided by meningeal lymphatic vessels. Furthermore, we delve into the mechanisms of crosstalk between meningeal lymphatic vessels and immune cells in the central nervous system under both homeostatic conditions and neurodegenerative diseases, discussing how these interactions shape the pathological outcomes. Regulation of meningeal lymphatic vessel function and structure can influence lymphatic drainage, cerebrospinal fluid-borne immune modulators, and immune cell populations in aging and neurodegenerative disorders, thereby playing a key role in shaping meningeal and brain parenchyma immunity.
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Affiliation(s)
- Minghuang Gao
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Xinyue Wang
- The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Shijie Su
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Weicheng Feng
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Yaona Lai
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Kongli Huang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Dandan Cao
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Qi Wang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 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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Hao M, Chu J, Zhang T, Yin T, Gu Y, Liang W, Ji W, Zhuang J, Liu Y, Gao J, Yin Y. Nanomaterials-mediated lysosomal regulation: a robust protein-clearance approach for the treatment of Alzheimer's disease. Neural Regen Res 2025; 20:424-439. [PMID: 38819046 DOI: 10.4103/nrr.nrr-d-23-01736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 02/20/2024] [Indexed: 06/01/2024] Open
Abstract
Alzheimer's disease is a debilitating, progressive neurodegenerative disorder characterized by the progressive accumulation of abnormal proteins, including amyloid plaques and intracellular tau tangles, primarily within the brain. Lysosomes, crucial intracellular organelles responsible for protein degradation, play a key role in maintaining cellular homeostasis. Some studies have suggested a link between the dysregulation of the lysosomal system and pathogenesis of neurodegenerative diseases, including Alzheimer's disease. Restoring the normal physiological function of lysosomes hold the potential to reduce the pathological burden and improve the symptoms of Alzheimer's disease. Currently, the efficacy of drugs in treating Alzheimer's disease is limited, with major challenges in drug delivery efficiency and targeting. Recently, nanomaterials have gained widespread use in Alzheimer's disease drug research owing to their favorable physical and chemical properties. This review aims to provide a comprehensive overview of recent advances in using nanomaterials (polymeric nanomaterials, nanoemulsions, and carbon-based nanomaterials) to enhance lysosomal function in treating Alzheimer's disease. This review also explores new concepts and potential therapeutic strategies for Alzheimer's disease through the integration of nanomaterials and modulation of lysosomal function. In conclusion, this review emphasizes the potential of nanomaterials in modulating lysosomal function to improve the pathological features of Alzheimer's disease. The application of nanotechnology to the development of Alzheimer's disease drugs brings new ideas and approaches for future treatment of this disease.
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Affiliation(s)
- Mengqi Hao
- Department of Neurology, Second Affiliated Hospital of Naval Medical University (Shanghai Changzheng Hospital), Shanghai, China
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Jianjian Chu
- Department of Neurology, Second Affiliated Hospital of Naval Medical University (Shanghai Changzheng Hospital), Shanghai, China
| | - Tinglin Zhang
- Changhai Clinical Research Unit, Shanghai Changhai Hospital, Naval Medical University, Shanghai, China
| | - Tong Yin
- Department of Neurology, Second Affiliated Hospital of Naval Medical University (Shanghai Changzheng Hospital), Shanghai, China
| | - Yuankai Gu
- Department of Neurology, Second Affiliated Hospital of Naval Medical University (Shanghai Changzheng Hospital), Shanghai, China
| | - Wendanqi Liang
- Department of Neurology, Second Affiliated Hospital of Naval Medical University (Shanghai Changzheng Hospital), Shanghai, China
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Wenbo Ji
- Department of Neurology, Second Affiliated Hospital of Naval Medical University (Shanghai Changzheng Hospital), Shanghai, China
| | - Jianhua Zhuang
- Department of Neurology, Second Affiliated Hospital of Naval Medical University (Shanghai Changzheng Hospital), Shanghai, China
| | - Yan Liu
- Department of Clinical Pharmacy, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Gao
- Changhai Clinical Research Unit, Shanghai Changhai Hospital, Naval Medical University, Shanghai, China
| | - You Yin
- Department of Neurology, Second Affiliated Hospital of Naval Medical University (Shanghai Changzheng Hospital), Shanghai, China
- Department of Neurology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
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Hu Z, Yang J, Zhang S, Li M, Zuo C, Mao C, Zhang Z, Tang M, Shi C, Xu Y. AAV mediated carboxyl terminus of Hsp70 interacting protein overexpression mitigates the cognitive and pathological phenotypes of APP/PS1 mice. Neural Regen Res 2025; 20:253-264. [PMID: 38767490 PMCID: PMC11246129 DOI: 10.4103/nrr.nrr-d-23-01277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/27/2023] [Accepted: 01/02/2024] [Indexed: 05/22/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202501000-00033/figure1/v/2024-05-14T021156Z/r/image-tiff The E3 ubiquitin ligase, carboxyl terminus of heat shock protein 70 (Hsp70) interacting protein (CHIP), also functions as a co-chaperone and plays a crucial role in the protein quality control system. In this study, we aimed to investigate the neuroprotective effect of overexpressed CHIP on Alzheimer's disease. We used an adeno-associated virus vector that can cross the blood-brain barrier to mediate CHIP overexpression in APP/PS1 mouse brain. CHIP overexpression significantly ameliorated the performance of APP/PS1 mice in the Morris water maze and nest building tests, reduced amyloid-β plaques, and decreased the expression of both amyloid-β and phosphorylated tau. CHIP also alleviated the concentration of microglia and astrocytes around plaques. In APP/PS1 mice of a younger age, CHIP overexpression promoted an increase in ADAM10 expression and inhibited β-site APP cleaving enzyme 1, insulin degrading enzyme, and neprilysin expression. Levels of HSP70 and HSP40, which have functional relevance to CHIP, were also increased. Single nuclei transcriptome sequencing in the hippocampus of CHIP overexpressed mice showed that the lysosomal pathway and oligodendrocyte-related biological processes were up-regulated, which may also reflect a potential mechanism for the neuroprotective effect of CHIP. Our research shows that CHIP effectively reduces the behavior and pathological manifestations of APP/PS1 mice. Indeed, overexpression of CHIP could be a beneficial approach for the treatment of Alzheimer's disease.
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Affiliation(s)
- Zhengwei Hu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Academy of Medical Sciences of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Jing Yang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- NHC Key Laboratory of Prevention and treatment of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Shuo Zhang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Academy of Medical Sciences of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Mengjie Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Chunyan Zuo
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Chengyuan Mao
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- NHC Key Laboratory of Prevention and treatment of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Zhongxian Zhang
- Sino-British Research Centre for Molecular Oncology, National Centre for International Research in Cell and Gene Therapy, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Mibo Tang
- Department of Gerontology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Changhe Shi
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- NHC Key Laboratory of Prevention and treatment of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Yuming Xu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- NHC Key Laboratory of Prevention and treatment of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, Henan Province, China
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7
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Liu J, Qiu S, Xue T, Yuan Y. Physiology and transcriptome of Eucommia ulmoides seeds at different germination stages. PLANT SIGNALING & BEHAVIOR 2024; 19:2329487. [PMID: 38493506 PMCID: PMC10950268 DOI: 10.1080/15592324.2024.2329487] [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: 10/13/2023] [Accepted: 01/03/2024] [Indexed: 03/19/2024]
Abstract
E. ulmoides (Eucommia ulmoides) has significant industrial and medicinal value and high market demand. E. ulmoides grows seedlings through sowing. According to previous studies, plant hormones have been shown to regulate seed germination. To understand the relationship between hormones and E. ulmoides seed germination, we focused on examining the changes in various indicators during the germination stage of E. ulmoides seeds. We measured the levels of physiological and hormone indicators in E. ulmoides seeds at different germination stages and found that the levels of abscisic acid (ABA), gibberellin (GA), and indole acetic acid (IAA) significantly varied as the seeds germinated. Furthermore, we confirmed that ABA, GA, and IAA are essential hormones in the germination of E. ulmoides seeds using Gene Ontology and Kyoto Encyclopedia of Genes and Genomics enrichment analyses of the transcriptome. The discovery of hormone-related synthesis pathways in the control group of Eucommia seeds at different germination stages further confirmed this conclusion. This study provides a basis for further research into the regulatory mechanisms of E. ulmoides seeds at different germination stages and the relationship between other seed germination and plant hormones.
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Affiliation(s)
- Jia Liu
- Department of Civil and Architecture and Engineering, Chuzhou University, Chuzhou, Anhui, China
- Anhui Low Carbon Highway Engineering Research Center, Chuzhou University, Anhui, China
| | - Sumei Qiu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Tingting Xue
- Department of Civil and Architecture and Engineering, Chuzhou University, Chuzhou, Anhui, China
| | - Yingdan Yuan
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
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8
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Gupta M, Dwivedi V, Kumar S, Patel A, Niazi P, Yadav VK. Lead toxicity in plants: mechanistic insights into toxicity, physiological responses of plants and mitigation strategies. PLANT SIGNALING & BEHAVIOR 2024; 19:2365576. [PMID: 38899525 PMCID: PMC11195469 DOI: 10.1080/15592324.2024.2365576] [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: 02/28/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024]
Abstract
Soil toxicity is a major environmental issue that leads to numerous harmful effects on plants and human beings. Every year a huge amount of Pb is dumped into the environment either from natural sources or anthropogenically. Being a heavy metal it is highly toxic and non-biodegradable but remains in the environment for a long time. It is considered a neurotoxic and exerts harmful effects on living beings. In the present review article, investigators have emphasized the side effects of Pb on the plants. Further, the authors have focused on the various sources of Pb in the environment. Investigators have emphasized the various responses including molecular, biochemical, and morphological of plants to the toxic levels of Pb. Further emphasis was given to the effect of elevated levels of Pb on the microbial population in the rhizospheres. Further, emphasized the various remediation strategies for the Pb removal from the soil and water sources.
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Affiliation(s)
- Minoti Gupta
- Department of Biotechnology, University Institute of Biotechnology, Chandigarh University, Chandigarh, Punjab, India
| | - Vinay Dwivedi
- Amity Institute of Biotechnology, Amity University, Gwalior, Madhya Pradesh, India
| | - Swatantar Kumar
- Department of Biotechnology Engineering and Food Technology, Chandigarh University, Chandigarh, Punjab, India
| | - Ashish Patel
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, Gujarat, India
| | - Parwiz Niazi
- Department of Biology, Faculty of Education, Kandahar University, Kandahar, Afghanistan
- Department of Plant Protection, Faculty of Agriculture, EGE University, İzmir, Turkey
| | - Virendra Kumar Yadav
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, Gujarat, India
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9
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Mihaylova NM, Manoylov IK, Nikolova MH, Prechl J, Tchorbanov AI. DNA and protein-generated chimeric molecules for delivery of influenza viral epitopes in mouse and humanized NSG transfer models. Hum Vaccin Immunother 2024; 20:2292381. [PMID: 38193304 DOI: 10.1080/21645515.2023.2292381] [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: 10/14/2023] [Accepted: 12/05/2023] [Indexed: 01/10/2024] Open
Abstract
Purified subunit viral antigens are weakly immunogenic and stimulate only the antibody but not the T cell-mediated immune response. An alternative approach to inducing protective immunity with small viral peptides may be the targeting of viral epitopes to immunocompetent cells by DNA and protein-engineered vaccines. This review will focus on DNA and protein-generated chimeric molecules carrying engineered fragments specific for activating cell surface co-receptors for inducing protective antiviral immunity. Adjuvanted protein-based vaccine or DNA constructs encoding simultaneously T- and B-cell peptide epitopes from influenza viral hemagglutinin, and scFvs specific for costimulatory immune cell receptors may induce a significant increase of anti-influenza antibody levels and strong CTL activity against virus-infected cells in a manner that mimics the natural infection. Here we summarize the development of several DNA and protein chimeric constructs carrying influenza virus HA317-41 fragment. The generated engineered molecules were used for immunization in intact murine and experimentally humanized NSG mouse models.
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Affiliation(s)
- Nikolina M Mihaylova
- Laboratory of Experimental Immunology, Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Iliyan K Manoylov
- Laboratory of Experimental Immunology, Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Maria H Nikolova
- National Reference Laboratory of Immunology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | - Andrey I Tchorbanov
- Laboratory of Experimental Immunology, Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
- National Institute of Immunology, Sofia, Bulgaria
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10
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Parves MR, Solares MJ, Dearnaley WJ, Kelly DF. Elucidating structural variability in p53 conformers using combinatorial refinement strategies and molecular dynamics. Cancer Biol Ther 2024; 25:2290732. [PMID: 38073067 PMCID: PMC10732606 DOI: 10.1080/15384047.2023.2290732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Low molecular weight proteins and protein assemblies can now be investigated using cryo-electron microscopy (EM) as a complement to traditional structural biology techniques. It is important, however, to not lose sight of the dynamic information inherent in macromolecules that give rise to their exquisite functionality. As computational methods continue to advance the field of biomedical imaging, so must strategies to resolve the minute details of disease-related entities. Here, we employed combinatorial modeling approaches to assess flexible properties among low molecular weight proteins (~100 kDa or less). Through a blend of rigid body refinement and simulated annealing, we determined new hidden conformations for wild type p53 monomer and dimer forms. Structures for both states converged to yield new conformers, each revealing good stereochemistry and dynamic information about the protein. Based on these insights, we identified fluid parts of p53 that complement the stable central core of the protein responsible for engaging DNA. Molecular dynamics simulations corroborated the modeling results and helped pinpoint the more flexible residues in wild type p53. Overall, the new computational methods may be used to shed light on other small protein features in a vast ensemble of structural data that cannot be easily delineated by other algorithms.
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Affiliation(s)
- Md Rimon Parves
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
- Biochemistry, Microbiology, and Molecular Biology Graduate Program, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Maria J. Solares
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
- Molecular, Cellular, and Integrative Biosciences Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - William J. Dearnaley
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
| | - Deborah F. Kelly
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
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11
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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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12
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Li T, Jia W, Peng S, Guo Y, Liu J, Zhang X, Li P, Zhang H, Xu R. Endogenous cAMP elevation in Brassica napus causes changes in phytohormone levels. PLANT SIGNALING & BEHAVIOR 2024; 19:2310963. [PMID: 38314783 PMCID: PMC10854363 DOI: 10.1080/15592324.2024.2310963] [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: 12/07/2023] [Accepted: 01/22/2024] [Indexed: 02/07/2024]
Abstract
In higher plants, the regulatory roles of cAMP (cyclic adenosine 3',5'-monophosphate) signaling remain elusive until now. Cellular cAMP levels are generally much lower in higher plants than in animals and transiently elevated for triggering downstream signaling events. Moreover, plant adenylate cyclase (AC) activities are found in different moonlighting multifunctional proteins, which may pose additional complications in distinguishing a specific signaling role for cAMP. Here, we have developed rapeseed (Brassica napus L.) transgenic plants that overexpress an inducible plant-origin AC activity for generating high AC levels much like that in animal cells, which served the genetic model disturbing native cAMP signaling as a whole in plants. We found that overexpression of the soluble AC activity had significant impacts on the contents of indole-3-acetic acid (IAA) and stress phytohormones, i.e. jasmonic acid (JA), abscisic acid (ABA), and salicylic acid (SA) in the transgenic plants. Acute induction of the AC activity caused IAA overaccumulation, and upregulation of TAA1 and CYP83B1 in the IAA biosynthesis pathways, but also simultaneously the hyper-induction of PR4 and KIN2 expression indicating activation of JA and ABA signaling pathways. We observed typical overgrowth phenotypes related to IAA excess in the transgenic plants, including significant increases in plant height, internode length, width of leaf blade, petiole length, root length, and fresh shoot biomass, as well as the precocious seed development, as compared to wild-type plants. In addition, we identified a set of 1465 cAMP-responsive genes (CRGs), which are most significantly enriched in plant hormone signal transduction pathway, and function mainly in relevance to hormonal, abiotic and biotic stress responses, as well as growth and development. Collectively, our results support that cAMP elevation impacts phytohormone homeostasis and signaling, and modulates plant growth and development. We proposed that cAMP signaling may be critical in configuring the coordinated regulation of growth and development in higher plants.
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Affiliation(s)
- Tianming Li
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wenjing Jia
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Song Peng
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Yanhui Guo
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Jinrui Liu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Xue Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Panyu Li
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Hanfeng Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Ruqiang Xu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
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13
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Sanjuan-Badillo A, P. Martínez-Castilla L, García-Sandoval R, Ballester P, Ferrándiz C, Sanchez MDLP, García-Ponce B, Garay-Arroyo A, R. Álvarez-Buylla E. HDACs MADS-domain protein interaction: a case study of HDA15 and XAL1 in Arabidopsis thaliana. PLANT SIGNALING & BEHAVIOR 2024; 19:2353536. [PMID: 38771929 PMCID: PMC11110687 DOI: 10.1080/15592324.2024.2353536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 05/01/2024] [Indexed: 05/23/2024]
Abstract
Cellular behavior, cell differentiation and ontogenetic development in eukaryotes result from complex interactions between epigenetic and classic molecular genetic mechanisms, with many of these interactions still to be elucidated. Histone deacetylase enzymes (HDACs) promote the interaction of histones with DNA by compacting the nucleosome, thus causing transcriptional repression. MADS-domain transcription factors are highly conserved in eukaryotes and participate in controlling diverse developmental processes in animals and plants, as well as regulating stress responses in plants. In this work, we focused on finding out putative interactions of Arabidopsis thaliana HDACs and MADS-domain proteins using an evolutionary perspective combined with bioinformatics analyses and testing the more promising predicted interactions through classic molecular biology tools. Through bioinformatic analyses, we found similarities between HDACs proteins from different organisms, which allowed us to predict a putative protein-protein interaction between the Arabidopsis thaliana deacetylase HDA15 and the MADS-domain protein XAANTAL1 (XAL1). The results of two-hybrid and Bimolecular Fluorescence Complementation analysis demonstrated in vitro and in vivo HDA15-XAL1 interaction in the nucleus. Likely, this interaction might regulate developmental processes in plants as is the case for this type of interaction in animals.
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Affiliation(s)
- Andrea Sanjuan-Badillo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Programa de Doctorado en Ciencias Biomédicas, de la Universidad Nacional Autónoma de México, Ciudad de México, México
| | - León P. Martínez-Castilla
- Investigadoras e Investigadores por México, Grupo de Genómica y Dinámica Evolutiva de Microorganismos Emergentes, Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
| | | | - Patricia Ballester
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV Universidad Politécnica de Valencia, Valencia, España
| | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV Universidad Politécnica de Valencia, Valencia, España
| | - Maria de la Paz Sanchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
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14
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Goodman RE. Twenty-eight years of GM Food and feed without harm: why not accept them? GM CROPS & FOOD 2024; 15:40-50. [PMID: 38471133 PMCID: PMC10939142 DOI: 10.1080/21645698.2024.2305944] [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: 07/31/2023] [Accepted: 01/11/2024] [Indexed: 03/14/2024]
Abstract
Since the first genetically engineered or modified crops or organisms (GMO) were approved for commercial production in 1995, no new GMO has been proven to be a hazard or cause harm to human consumers. These modifications have improved crop efficiency, reduced losses to insect pests, reduced losses to viral and microbial plant pathogens and improved drought tolerance. A few have focused on nutritional improvements producing beta carotene in Golden Rice. Regulators in the United States and countries signing the CODEX Alimentarius and Cartagena Biosafety agreements have evaluated human and animal food safety considering potential risks of allergenicity, toxicity, nutritional and anti-nutritional risks. They consider risks for non-target organisms and the environment. There are no cases where post-market surveillance has uncovered harm to consumers or the environment including potential transfer of DNA from the GMO to non-target organisms. In fact, many GMOs have helped improve production, yield and reduced risks from chemical insecticides or fungicides. Yet there are generic calls to label foods containing any genetic modification as a GMO and refusing to allow GM events to be labeled as organic. Many African countries have accepted the Cartagena Protocol as a tool to keep GM events out of their countries while facing food insecurity. The rationale for those restrictions are not rational. Other issues related to genetic diversity, seed production and environmental safety must be addressed. What can be done to increase acceptance of safe and nutritious foods as the population increases, land for cultivation is reduced and energy costs soar?
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Affiliation(s)
- Richard E. Goodman
- Food Allergy Research and Resource Program, Department of Food Science, University of Nebraska-Lincoln, Lincoln, NE, USA
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15
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Yao R, Xie C, Xia X. Recent progress in mRNA cancer vaccines. Hum Vaccin Immunother 2024; 20:2307187. [PMID: 38282471 PMCID: PMC10826636 DOI: 10.1080/21645515.2024.2307187] [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: 09/28/2023] [Accepted: 01/16/2024] [Indexed: 01/30/2024] Open
Abstract
The research and development of messenger RNA (mRNA) cancer vaccines have gradually overcome numerous challenges through the application of personalized cancer antigens, structural optimization of mRNA, and the development of alternative RNA-based vectors and efficient targeted delivery vectors. Clinical trials are currently underway for various cancer vaccines that encode tumor-associated antigens (TAAs), tumor-specific antigens (TSAs), or immunomodulators. In this paper, we summarize the optimization of mRNA and the emergence of RNA-based expression vectors in cancer vaccines. We begin by reviewing the advancement and utilization of state-of-the-art targeted lipid nanoparticles (LNPs), followed by presenting the primary classifications and clinical applications of mRNA cancer vaccines. Collectively, mRNA vaccines are emerging as a central focus in cancer immunotherapy, offering the potential to address multiple challenges in cancer treatment, either as standalone therapies or in combination with current cancer treatments.
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Affiliation(s)
- Ruhui Yao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Chunyuan Xie
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiaojun Xia
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
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16
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Qu Y, Zeng A, Cheng Y, Li S. Natural killer cell memory: challenges and opportunities for cancer immunotherapy. Cancer Biol Ther 2024; 25:2376410. [PMID: 38987282 PMCID: PMC11238922 DOI: 10.1080/15384047.2024.2376410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 07/01/2024] [Indexed: 07/12/2024] Open
Abstract
Substantial advancements have been made in recent years in comprehending immune memory, which enhances the secondary response through prior infections. The ability of vertebrate T and B lymphocytes to exhibit classic recall responses has long been regarded as a distinguishing characteristic. However, natural killer (NK) cells have been found to acquire immunological memory in a manner akin to T and B cells. The fundamental principles derived from the investigation of NK cell memory offer novel insights into innate immunity and have the potential to pave the way for innovative strategies to enhance therapeutic interventions against multiple diseases including cancer. Here, we reviewed the fundamental characteristics, memory development and regulatory mechanism of NK cell memory. Moreover, we will conduct a comprehensive evaluation of the accomplishments, obstacles, and future direction pertaining to the utilization of NK cell memory in the field of cancer immunotherapy.
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Affiliation(s)
- Yuhua Qu
- Department of Anorectal Surgery, Hospital of Chengdu University of Traditional Chinese Medicine and Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Anhui Zeng
- Department of Anorectal Surgery, Hospital of Chengdu University of Traditional Chinese Medicine and Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yulu Cheng
- Department of Disinfection Supply Center, Hospital of Chengdu University of Traditional Chinese Medicine and Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shengchun Li
- Department of Anorectal Surgery, Hospital of Chengdu University of Traditional Chinese Medicine and Chengdu University of Traditional Chinese Medicine, Chengdu, China
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17
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Cha M, Kim JK, Lee WH, Song H, Lee TG, Kim SK, Kim SJ. Metabolic engineering of Caldicellulosiruptor bescii for hydrogen production. Appl Microbiol Biotechnol 2024; 108:65. [PMID: 38194138 PMCID: PMC10776719 DOI: 10.1007/s00253-023-12974-7] [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: 10/07/2023] [Revised: 12/04/2023] [Accepted: 12/15/2023] [Indexed: 01/10/2024]
Abstract
Hydrogen is an alternative fuel for transportation vehicles because it is clean, sustainable, and highly flammable. However, the production of hydrogen from lignocellulosic biomass by microorganisms presents challenges. This microbial process involves multiple complex steps, including thermal, chemical, and mechanical treatment of biomass to remove hemicellulose and lignin, as well as enzymatic hydrolysis to solubilize the plant cell walls. These steps not only incur costs but also result in the production of toxic hydrolysates, which inhibit microbial growth. A hyper-thermophilic bacterium of Caldicellulosiruptor bescii can produce hydrogen by decomposing and fermenting plant biomass without the need for conventional pretreatment. It is considered as a consolidated bioprocessing (CBP) microorganism. This review summarizes the basic scientific knowledge and hydrogen-producing capacity of C. bescii. Its genetic system and metabolic engineering strategies to improve hydrogen production are also discussed. KEY POINTS: • Hydrogen is an alternative and eco-friendly fuel. • Caldicellulosiruptor bescii produces hydrogen with a high yield in nature. • Metabolic engineering can make C. bescii to improve hydrogen production.
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Affiliation(s)
- Minseok Cha
- Research Center for Biological Cybernetics, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Jung Kon Kim
- Department of Animal Environment, National Institute of Animal Science, Wanju, 55365, Republic of Korea
| | - Won-Heong Lee
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | | | - Tae-Gi Lee
- Department of Food Science and Biotechnology, Chung-Ang University, Gyeonggi, 17546, Republic of Korea
| | - Sun-Ki Kim
- Department of Food Science and Biotechnology, Chung-Ang University, Gyeonggi, 17546, Republic of Korea
| | - Soo-Jung Kim
- Research Center for Biological Cybernetics, Chonnam National University, Gwangju, 61186, Republic of Korea.
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, 61186, Republic of Korea.
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18
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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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19
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Alhazmi AI, El-Refaei MF, Abdallah EAA. Protective effects of gallic acid against nickel-induced kidney injury: impact of antioxidants and transcription factor on the incidence of nephrotoxicity. Ren Fail 2024; 46:2344656. [PMID: 38685608 PMCID: PMC11062283 DOI: 10.1080/0886022x.2024.2344656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 04/14/2024] [Indexed: 05/02/2024] Open
Abstract
Nickel (Ni) is a common metal with a nephrotoxic effect, damaging the kidneys. This study investigated the mechanism by which gallic acid (GA) protects mice kidneys against renal damage induced by Nickel oxide nanoparticles (NiO-NPs). Forty male Swiss albino mice were randomly assigned into four groups, each consisting of ten mice (n = 10/group): Group I the control group, received no treatment; Group II, the GA group, was administrated GA at a dosage of 110 mg/kg/day body weight; Group III, the NiO-NPs group, received injection of NiO-NPs at a concentration of 20 mg/kg body weight for 10 consecutive days; Group IV, the GA + NiO-NPs group, underwent treatment with both GA and NiO-NPs. The results showed a significant increase in serum biochemical markers and a reduction in antioxidant activities. Moreover, levels of 8-hydroxy-2'-deoxyguanosine (8-OH-dG), phosphorylated nuclear factor kappa B (p65), and protein carbonyl (PC) were significantly elevated in group III compared with group I. Furthermore, the western blot analysis revealed significant high NF-κB p65 expression, immunohistochemistry of the NF-κB and caspase-1 expression levels were significantly increased in group III compared to group I. Additionally, the histopathological inspection of the kidney in group III exhibited a substantial increase in extensive necrosis features compared with group I. In contrast, the concomitant coadministration of GA and NiO-NPs in group IV showed significant biochemical, antioxidant activities, immunohistochemical and histopathological improvements compared with group III. Gallic acid has a protective role against kidney dysfunction and renal damage in Ni-nanoparticle toxicity.
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Affiliation(s)
| | - Mohamed F. El-Refaei
- Faculty of Medicine, Al-Baha University, Al Baha, Saudi Arabia
- Biochemistry and Molecular Biology, Genetic Institute, Sadat City University, Sadat City, Egypt
| | - Eman A. A. Abdallah
- Faculty of Medicine, Al-Baha University, Al Baha, Saudi Arabia
- Forensic Medicine and Clinical Toxicology, Faculty of Medicine, Zagazig University, Egypt
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20
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Arancibia F, De Giorgis D, Medina F, Hermosilla T, Simon F, Varela D. Role of the Ca V1.2 distal carboxy terminus in the regulation of L-type current. Channels (Austin) 2024; 18:2338782. [PMID: 38691022 PMCID: PMC11067984 DOI: 10.1080/19336950.2024.2338782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 03/31/2024] [Indexed: 05/03/2024] Open
Abstract
L-type calcium channels are essential for the excitation-contraction coupling in cardiac muscle. The CaV1.2 channel is the most predominant isoform in the ventricle which consists of a multi-subunit membrane complex that includes the CaV1.2 pore-forming subunit and auxiliary subunits like CaVα2δ and CaVβ2b. The CaV1.2 channel's C-terminus undergoes proteolytic cleavage, and the distal C-terminal domain (DCtermD) associates with the channel core through two domains known as proximal and distal C-terminal regulatory domain (PCRD and DCRD, respectively). The interaction between the DCtermD and the remaining C-terminus reduces the channel activity and modifies voltage- and calcium-dependent inactivation mechanisms, leading to an autoinhibitory effect. In this study, we investigate how the interaction between DCRD and PCRD affects the inactivation processes and CaV1.2 activity. We expressed a 14-amino acid peptide miming the DCRD-PCRD interaction sequence in both heterologous systems and cardiomyocytes. Our results show that overexpression of this small peptide can displace the DCtermD and replicate the effects of the entire DCtermD on voltage-dependent inactivation and channel inhibition. However, the effect on calcium-dependent inactivation requires the full DCtermD and is prevented by overexpression of calmodulin. In conclusion, our results suggest that the interaction between DCRD and PCRD is sufficient to bring about the current inhibition and alter the voltage-dependent inactivation, possibly in an allosteric manner. Additionally, our data suggest that the DCtermD competitively modifies the calcium-dependent mechanism. The identified peptide sequence provides a valuable tool for further dissecting the molecular mechanisms that regulate L-type calcium channels' basal activity in cardiomyocytes.
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Affiliation(s)
- Felipe Arancibia
- Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Chile, Santiago, Chile
- Programa de Fisiología y Biofísica, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Daniela De Giorgis
- Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Chile, Santiago, Chile
- Programa de Fisiología y Biofísica, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Franco Medina
- Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Chile, Santiago, Chile
- Programa de Fisiología y Biofísica, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Tamara Hermosilla
- Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Chile, Santiago, Chile
- Programa de Fisiología y Biofísica, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Felipe Simon
- Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Chile, Santiago, Chile
- Laboratory of Integrative Physiopathology, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Diego Varela
- Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Chile, Santiago, Chile
- Programa de Fisiología y Biofísica, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
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21
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Xu H, Du Z, Li Z, Liu X, Li X, Zhang X, Ma J. MUC1-EGFR crosstalk with IL-6 by activating NF-κB and MAPK pathways to regulate the stemness and paclitaxel-resistance of lung adenocarcinoma. Ann Med 2024; 56:2313671. [PMID: 38325364 PMCID: PMC10851807 DOI: 10.1080/07853890.2024.2313671] [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: 09/19/2023] [Accepted: 01/24/2024] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND The chemotherapy resistance often leads to chemotherapy failure. This study aims to explore the molecular mechanism by which MUC1 regulates paclitaxel resistance in lung adenocarcinoma (LUAD), providing scientific basis for future target selection. METHODS The bioinformatics method was used to analyse the mRNA and protein expression characteristics of MUC1 in LUAD. RT-qPCR and ELISA were used to detect the mRNA and protein expression, flow cytometry was used to detect CD133+ cells, and cell viability was detected by CCK-8 assay. The mRNA-seq was performed to analyse the changes in expression profile, GO and KEGG analysis were used to explore the potential biological functions. RESULTS MUC1 is highly expressed in LUAD patients and is associated with a higher tumour infiltration. In paclitaxel resistance LUAD cells (A549/TAX cells), the expression of MUC1, EGFR/p-EGFR and IL-6 were higher than that of A549 cells, the proportion of CD133+ cells was significantly increased, and the expression of cancer stem cell (CSCs) transcription factors (NANOG, OCT4 and SOX2) were significantly up-regulated. After knocking down MUC1 in A549/Tax cells, the activity of A549/Tax cells was significantly decreased. Correspondingly, the expression of EGFR, IL-6, OCT4, NANOG, and SOX2 were significantly down-regulated. The mRNA-seq showed that knocking down MUC1 affected the gene expression, DEGs mainly enriched in NF-κB and MAPK signalling pathway. CONCLUSION MUC1 was highly expressed in A549/TAX cells, and MUC1-EGFR crosstalk with IL-6 may be due to the activation of NF-κB and MAPK pathways, which promote the enrichment of CSCs and lead to paclitaxel resistance.
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Affiliation(s)
- Hongyu Xu
- Department of Oncology, 363 Hospital, Chengdu, Sichuan, P.R. China
| | - Zedong Du
- Department of Oncology, Chengdu Second People’s Hospital, Chengdu, Sichuan, P.R. China
| | - Zhihui Li
- Department of Oncology, The General Hospital of Western Theater Command of PLA, Chengdu, Sichuan, P.R. China
| | - Xianguo Liu
- Department of Oncology, 363 Hospital, Chengdu, Sichuan, P.R. China
| | - Xueting Li
- Department of Oncology, 363 Hospital, Chengdu, Sichuan, P.R. China
| | - Xuan Zhang
- Science and Education Department, 363 Hospital, Chengdu, Sichuan, P.R. China
| | - Jiayu Ma
- Department of Oncology, 363 Hospital, Chengdu, Sichuan, P.R. China
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22
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Keeley O, Coyne AN. Nuclear and degradative functions of the ESCRT-III pathway: implications for neurodegenerative disease. Nucleus 2024; 15:2349085. [PMID: 38700207 PMCID: PMC11073439 DOI: 10.1080/19491034.2024.2349085] [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: 02/11/2024] [Accepted: 04/24/2024] [Indexed: 05/05/2024] Open
Abstract
The ESCRT machinery plays a pivotal role in membrane-remodeling events across multiple cellular processes including nuclear envelope repair and reformation, nuclear pore complex surveillance, endolysosomal trafficking, and neuronal pruning. Alterations in ESCRT-III functionality have been associated with neurodegenerative diseases including Frontotemporal Dementia (FTD), Amyotrophic Lateral Sclerosis (ALS), and Alzheimer's Disease (AD). In addition, mutations in specific ESCRT-III proteins have been identified in FTD/ALS. Thus, understanding how disruptions in the fundamental functions of this pathway and its individual protein components in the human central nervous system (CNS) may offer valuable insights into mechanisms underlying neurodegenerative disease pathogenesis and identification of potential therapeutic targets. In this review, we discuss ESCRT components, dynamics, and functions, with a focus on the ESCRT-III pathway. In addition, we explore the implications of altered ESCRT-III function for neurodegeneration with a primary emphasis on nuclear surveillance and endolysosomal trafficking within the CNS.
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Affiliation(s)
- Olivia Keeley
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alyssa N. Coyne
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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23
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Trus M, Atlas D. Non-ionotropic voltage-gated calcium channel signaling. Channels (Austin) 2024; 18:2341077. [PMID: 38601983 PMCID: PMC11017947 DOI: 10.1080/19336950.2024.2341077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024] Open
Abstract
Voltage-gated calcium channels (VGCCs) are the major conduits for calcium ions (Ca2+) within excitable cells. Recent studies have highlighted the non-ionotropic functionality of VGCCs, revealing their capacity to activate intracellular pathways independently of ion flow. This non-ionotropic signaling mode plays a pivotal role in excitation-coupling processes, including gene transcription through excitation-transcription (ET), synaptic transmission via excitation-secretion (ES), and cardiac contraction through excitation-contraction (EC). However, it is noteworthy that these excitation-coupling processes require extracellular calcium (Ca2+) and Ca2+ occupancy of the channel ion pore. Analogous to the "non-canonical" characterization of the non-ionotropic signaling exhibited by the N-methyl-D-aspartate receptor (NMDA), which requires extracellular Ca2+ without the influx of ions, VGCC activation requires depolarization-triggered conformational change(s) concomitant with Ca2+ binding to the open channel. Here, we discuss the contributions of VGCCs to ES, ET, and EC coupling as Ca2+ binding macromolecules that transduces external stimuli to intracellular input prior to elevating intracellular Ca2+. We emphasize the recognition of calcium ion occupancy within the open ion-pore and its contribution to the excitation coupling processes that precede the influx of calcium. The non-ionotropic activation of VGCCs, triggered by the upstroke of an action potential, provides a conceptual framework to elucidate the mechanistic aspects underlying the microseconds nature of synaptic transmission, cardiac contractility, and the rapid induction of first-wave genes.
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Affiliation(s)
- Michael Trus
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Daphne Atlas
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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24
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King MR, Ruff KM, Pappu RV. Emergent microenvironments of nucleoli. Nucleus 2024; 15:2319957. [PMID: 38443761 PMCID: PMC10936679 DOI: 10.1080/19491034.2024.2319957] [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: 09/04/2023] [Accepted: 02/13/2024] [Indexed: 03/07/2024] Open
Abstract
In higher eukaryotes, the nucleolus harbors at least three sub-phases that facilitate multiple functionalities including ribosome biogenesis. The three prominent coexisting sub-phases are the fibrillar center (FC), the dense fibrillar component (DFC), and the granular component (GC). Here, we review recent efforts in profiling sub-phase compositions that shed light on the types of physicochemical properties that emerge from compositional biases and territorial organization of specific types of macromolecules. We highlight roles played by molecular grammars which refers to protein sequence features including the substrate binding domains, the sequence features of intrinsically disordered regions, and the multivalence of these distinct types of domains / regions. We introduce the concept of a barcode of emergent physicochemical properties of nucleoli. Although our knowledge of the full barcode remains incomplete, we hope that the concept prompts investigations into undiscovered emergent properties and engenders an appreciation for how and why unique microenvironments control biochemical reactions.
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Affiliation(s)
- Matthew R. King
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Campus, MO, USA
| | - Kiersten M. Ruff
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Campus, MO, USA
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Campus, MO, USA
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25
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Bu C, Wang Z, Lv X, Zhao Y. A dual-gene panel of two fragments of methylated IRF4 and one of ZEB2 in plasma cell-free DNA for gastric cancer detection. Epigenetics 2024; 19:2374988. [PMID: 39003776 PMCID: PMC11249030 DOI: 10.1080/15592294.2024.2374988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/26/2024] [Indexed: 07/16/2024] Open
Abstract
Early detection is crucial for increasing the survival rate of gastric cancer (GC). We aimed to identify a methylated cell-free DNA (cfDNA) marker panel for detecting GC. The differentially methylated CpGs (DMCs) were selected from datasets of The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The selected DMCs were validated and further selected in tissue samples (40 gastric cancer and 36 healthy white blood cell samples) and in a quarter sample volume of plasma samples (37 gastric cancer, 12 benign gastric disease, and 43 healthy individuals). The marker combination selected was then evaluated in a normal sample volume of plasma samples (35 gastric cancer, 39 control diseases, and 40 healthy individuals) using real-time methylation-specific PCR (MSP). The analysis of the results compared methods based on 2-ΔΔCt values and Ct values. In the results, 30 DMCs were selected through bioinformatics methods, and then 5 were selected for biological validation. The marker combination of two fragments of IRF4 (IRF4-1 and IRF4-2) and one of ZEB2 was selected due to its good performance. The Ct-based method was selected for its good results and practical advantages. The assay, IRF4-1 and IRF4-2 in one fluorescence channel and ZEB2 in another, obtained 74.3% sensitivity for the GC group at any stage, at 92.4% specificity. In conclusion, the panel of IRF4 and ZEB2 in plasma cfDNA demonstrates good diagnostic performance and application potential in clinical settings.
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Affiliation(s)
- Chunxiao Bu
- Department of Magnetic Resonance Imaging,The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zhilong Wang
- Henan Academy of Medical Sciences, Zhengzhou, Henan, China
| | - Xianping Lv
- Department of Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yanteng Zhao
- Department of Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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26
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Makeyev EV, Huang S. The perinucleolar compartment: structure, function, and utility in anti-cancer drug development. Nucleus 2024; 15:2306777. [PMID: 38281066 PMCID: PMC10824145 DOI: 10.1080/19491034.2024.2306777] [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: 09/25/2023] [Accepted: 01/12/2024] [Indexed: 01/29/2024] Open
Abstract
The perinucleolar compartment (PNC) was initially identified as a nuclear structure enriched for the polypyrimidine tract-binding protein. Since then, the PNC has been implicated in carcinogenesis. The prevalence of this compartment is positively correlated with disease progression in various types of cancer, and its expression in primary tumors is linked to worse patient outcomes. Using the PNC as a surrogate marker for anti-cancer drug efficacy has led to the development of a clinical candidate for anti-metastasis therapies. The PNC is a multicomponent nuclear body situated at the periphery of the nucleolus. Thus far, several non-coding RNAs and RNA-binding proteins have been identified as the PNC components. Here, we summarize the current understanding of the structure and function of the PNC, as well as its recurrent links to cancer progression and metastasis.
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Affiliation(s)
- Eugene V. Makeyev
- Centre for Developmental Neurobiology, King’s College London, London, UK
| | - Sui Huang
- Department of Cell and Developmental Biology, Northwestern University, Chicago, IL, USA
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27
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Zhao Y, Zhao L, Jin H, Xie Y, Chen L, Zhang W, Dong L, Zhang L, Huang Y, Wan K, Yang Q, Wang S. Plasma methylated GNB4 and Riplet as a novel dual-marker panel for the detection of hepatocellular carcinoma. Epigenetics 2024; 19:2299044. [PMID: 38154055 PMCID: PMC10761049 DOI: 10.1080/15592294.2023.2299044] [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: 12/19/2023] [Indexed: 12/30/2023] Open
Abstract
Early detection of hepatocellular carcinoma (HCC) can greatly improve the survival rate of patients. We aimed to develop a novel marker panel based on cell-free DNA (cfDNA) methylation for the detection of HCC. The differentially methylated CpG sites (DMCs) specific for HCC blood diagnosis were selected from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, then validated by the whole genome bisulphite sequencing (WGBS) of 12 paired HCC and paracancerous tissues. The clinical performance of the panel was evaluated using tissue samples [32 HCC, chronic liver disease (CLD), and healthy individuals] and plasma cohorts (173 HCC, 199 CLD, and 98 healthy individuals). The combination of G protein subunit beta 4 (GNB4) and Riplet had the optimal area under the curve (AUC) in seven candidates through TCGA, GEO, and WGBS analyses. In tissue validation, the GNB4 and Riplet showed an AUC of 100% with a sensitivity and specificity of 100% for detecting any-stage HCC. In plasma, it demonstrated a high sensitivity of 84.39% at 91.92% specificity, with an AUC of 92.51% for detecting any-stage HCC. The dual-marker panel had a higher sensitivity of 78.26% for stage I HCC than alpha-fetoprotein (AFP) of 47.83%, and a high sensitivity of 70.27% for detecting a single tumour (size ≤3 cm). In conclusion, we developed a novel dual-marker panel that demonstrates high accuracy in detecting HCC, surpassing the performance of AFP testing.
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Affiliation(s)
- Yanteng Zhao
- Department of Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lei Zhao
- Plastic maxillofacial surgery, Jiangxi Provincial People’s Hospital, Nanchang, Jiangxi, China
| | - Huifang Jin
- Department of Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Ying Xie
- Department of Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Liyinghui Chen
- Department of Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Wei Zhang
- Research and development department, Wuhan Ammunition Life-tech Company, Ltd., Wuhan, Hubei, China
| | - Lanlan Dong
- Research and development department, Wuhan Ammunition Life-tech Company, Ltd., Wuhan, Hubei, China
| | - Lianglu Zhang
- Research and development department, Wuhan Ammunition Life-tech Company, Ltd., Wuhan, Hubei, China
| | - Yue Huang
- Research and development department, Wuhan Ammunition Life-tech Company, Ltd., Wuhan, Hubei, China
| | - Kangkang Wan
- Research and development department, Wuhan Ammunition Life-tech Company, Ltd., Wuhan, Hubei, China
| | - Qiankun Yang
- Department of Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Shaochi Wang
- Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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28
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Meng P, Liu C, Li J, Fang P, Yang B, Sun W, Zhang Y. CXC chemokine receptor 7 ameliorates renal fibrosis by inhibiting β-catenin signaling and epithelial-to-mesenchymal transition in tubular epithelial cells. Ren Fail 2024; 46:2300727. [PMID: 38189094 PMCID: PMC10776045 DOI: 10.1080/0886022x.2023.2300727] [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: 05/04/2023] [Accepted: 12/26/2023] [Indexed: 01/09/2024] Open
Abstract
Renal fibrosis is a common feature of various chronic kidney diseases. However, the underlying mechanism remains poorly understood. The CXC chemokine receptor (CXCR) family plays a role in renal fibrosis; however, the detailed mechanisms have not been elucidated. In this study, we investigated the potential role of CXCR7 in mediating renal fibrosis. CXCR7 expression is decreased in unilateral ischemia-reperfusion injury (UIRI) and unilateral ureteral obstruction mouse models. Furthermore, CXCR7 was specifically expressed primarily in the Lotus Tetragonolobus Lectin-expressing segment of tubules, was slightly expressed in the peanut agglutinin-expressing segment, and was barely expressed in the Dolichos biflorus agglutinin-expressing segment. Administration of pFlag-CXCR7, an overexpression plasmid for CXCR7, significantly inhibited the activation of β-catenin signaling and protected against the progression of epithelial-to-mesenchymal transition (EMT) and renal fibrosis in a UIRI mouse model. Using cultured HKC-8 cells, we found that CXCR7 significantly downregulated the expression of active β-catenin and fibrosis-related markers, including fibronectin, Collagen I, and α-SMA. Furthermore, CXCR7 significantly attenuated TGF-β1-induced changes in β-catenin signaling, EMT and fibrosis. These results suggest that CXCR7 plays a crucial role in inhibiting the activation of β-catenin signaling and the progression of EMT and renal fibrosis. Thus, CXCR7 could be a novel therapeutic target for renal fibrosis.
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Affiliation(s)
- Ping Meng
- Department of Central Laboratory, Huadu District People’s Hospital of Guangzhou, Guangzhou, China
| | - Chunli Liu
- Department of Central Laboratory, Huadu District People’s Hospital of Guangzhou, Guangzhou, China
| | - Jingchun Li
- Department of Central Laboratory, Huadu District People’s Hospital of Guangzhou, Guangzhou, China
| | - Ping Fang
- Department of Laboratory Medicine, Huadu District People’s Hospital of Guangzhou, Guangzhou, China
| | - Bo Yang
- Department of Clinical Nutrition, Huadu District People’s Hospital of Guangzhou, Guangzhou, China
| | - Wei Sun
- Department of Central Laboratory, Huadu District People’s Hospital of Guangzhou, Guangzhou, China
| | - Yunfang Zhang
- Department of Nephrology, Huadu District People’s Hospital of Guangzhou, Guangzhou, China
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29
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Shi A, Yun F, Shi L, Liu X, Jia Y. Research progress on the mechanism of common inflammatory pathways in the pathogenesis and development of lymphoma. Ann Med 2024; 56:2329130. [PMID: 38489405 PMCID: PMC10946270 DOI: 10.1080/07853890.2024.2329130] [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: 08/22/2023] [Accepted: 02/25/2024] [Indexed: 03/17/2024] Open
Abstract
In recent years, the incidence and mortality rates of lymphoma have gradually increased worldwide. Tumorigenesis and drug resistance are closely related to intracellular inflammatory pathways in lymphoma. Therefore, understanding the biological role of inflammatory pathways and their abnormal activation in relation to the development of lymphoma and their selective modulation may open new avenues for targeted therapy of lymphoma. The biological functions of inflammatory pathways are extensive, and they are central hubs for regulating inflammatory responses, immune responses, and the tumour immune microenvironment. However, limited studies have investigated the role of inflammatory pathways in lymphoma development. This review summarizes the relationship between abnormal activation of common inflammatory pathways and lymphoma development to identify precise and efficient targeted therapeutic options for patients with advanced, drug-resistant lymphoma.
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Affiliation(s)
- Aorong Shi
- Department of Pathology, Basic Medical Sciences College, Inner Mongolia Medical University, Hohhot, China
| | - Fen Yun
- Department of Pathology, Basic Medical Sciences College, Inner Mongolia Medical University, Hohhot, China
- Department of Pathology, The First Affiliated Hospital of Inner Mongolia Medical University, Huhhot, China
| | - Lin Shi
- Department of Pathology, Basic Medical Sciences College, Inner Mongolia Medical University, Hohhot, China
- Department of Pathology, The First Affiliated Hospital of Inner Mongolia Medical University, Huhhot, China
| | - Xia Liu
- Department of Pathology, Basic Medical Sciences College, Inner Mongolia Medical University, Hohhot, China
- Department of Pathology, The First Affiliated Hospital of Inner Mongolia Medical University, Huhhot, China
| | - Yongfeng Jia
- Department of Pathology, Basic Medical Sciences College, Inner Mongolia Medical University, Hohhot, China
- Department of Pathology, The First Affiliated Hospital of Inner Mongolia Medical University, Huhhot, China
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30
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Mars JC, Culjkovic-Kraljacic B, Borden KL. eIF4E orchestrates mRNA processing, RNA export and translation to modify specific protein production. Nucleus 2024; 15:2360196. [PMID: 38880976 PMCID: PMC11185188 DOI: 10.1080/19491034.2024.2360196] [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: 02/12/2024] [Accepted: 05/22/2024] [Indexed: 06/18/2024] Open
Abstract
The eukaryotic translation initiation factor eIF4E acts as a multifunctional factor that simultaneously influences mRNA processing, export, and translation in many organisms. Its multifactorial effects are derived from its capacity to bind to the methyl-7-guanosine cap on the 5'end of mRNAs and thus can act as a cap chaperone for transcripts in the nucleus and cytoplasm. In this review, we describe the multifactorial roles of eIF4E in major mRNA-processing events including capping, splicing, cleavage and polyadenylation, nuclear export and translation. We discuss the evidence that eIF4E acts at two levels to generate widescale changes to processing, export and ultimately the protein produced. First, eIF4E alters the production of components of the mRNA processing machinery, supporting a widescale reprogramming of multiple mRNA processing events. In this way, eIF4E can modulate mRNA processing without physically interacting with target transcripts. Second, eIF4E also physically interacts with both capped mRNAs and components of the RNA processing or translation machineries. Further, specific mRNAs are sensitive to eIF4E only in particular mRNA processing events. This selectivity is governed by the presence of cis-acting elements within mRNAs known as USER codes that recruit relevant co-factors engaging the appropriate machinery. In all, we describe the molecular bases for eIF4E's multifactorial function and relevant regulatory pathways, discuss the basis for selectivity, present a compendium of ~80 eIF4E-interacting factors which play roles in these activities and provide an overview of the relevance of its functions to its oncogenic potential. Finally, we summarize early-stage clinical studies targeting eIF4E in cancer.
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Affiliation(s)
- Jean-Clément Mars
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Montréal, QC, Canada
| | - Biljana Culjkovic-Kraljacic
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Montréal, QC, Canada
| | - Katherine L.B. Borden
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Montréal, QC, Canada
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31
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Xia YM, Guan YQ, Liang JF, Wu WD. TAK-242 improves sepsis-associated acute kidney injury in rats by inhibiting the TLR4/NF-κB signaling pathway. Ren Fail 2024; 46:2313176. [PMID: 38482886 PMCID: PMC10877656 DOI: 10.1080/0886022x.2024.2313176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 01/27/2024] [Indexed: 03/18/2024] Open
Abstract
OBJECTIVE This study was designed to observe the effect of toll-like receptor 4 (TLR4)/nuclear factor kappa-B (NF-κB) pathway activity on sepsis-associated acute kidney injury (SA-AKI), thereby providing new considerations for the prevention and treatment of SA-AKI. METHODS The rats were divided into Sham, cecal ligation and puncture (CLP), CLP + vehicle, and CLP + TAK-242 groups. Except the Sham group, a model of CLP-induced sepsis was established in other groups. After 24 h, the indicators related to kidney injury in blood samples were detected. The pathological changes in the kidneys were observed by hematoxylin-eosin staining, and tubular damage was scored. Oxidative stress-related factors, mitochondrial dysfunction-related indicators in each group were measured; the levels of inflammatory factors in serum and kidney tissue of rats were examined. Finally, the expression of proteins related to the TLR4/NF-κB signaling pathway was observed by western blot. RESULTS Compared with the CLP + vehicle and CLP + TAK-242 groups, the CLP + TAK-242 group reduced blood urea nitrogen (BUN), creatinine (Cr), cystatin-C (Cys-C), reactive oxygen species (ROS), malondialdehyde (MDA), and inflammatory factors levels (p < 0.01), as well as increased superoxide dismutase (SOD) activity of CLP rats (p < 0.01). Additionally, TAK-242 treatment improved the condition of CLP rats that had glomerular and tubular injuries and mitochondrial disorders (p < 0.01). Further mechanism research revealed that TAK-242 can inhibit the TLR4/NF-κB signaling pathway activated by CLP (p < 0.01). Above indicators after TAK-242 treatment were close to those of the Sham group. CONCLUSION TAK-242 can improve oxidative stress, mitochondrial dysfunction, and inflammatory response by inhibiting the activity of TLR4/NF-κB signaling pathway, thereby preventing rats from SA-AKI.
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Affiliation(s)
- Yan-mei Xia
- Department of Critical, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, PRChina
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PRChina
| | - Yu-qian Guan
- Department of Critical, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, PRChina
| | - Ji-fang Liang
- Department of Critical, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, PRChina
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PRChina
| | - Wei-dong Wu
- Department of Critical, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, PRChina
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PRChina
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32
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Kumari P, Yadav S, Sarkar S, Satheeshkumar PK. Cleavage of cell junction proteins as a host invasion strategy in leptospirosis. Appl Microbiol Biotechnol 2024; 108:119. [PMID: 38204132 PMCID: PMC10781872 DOI: 10.1007/s00253-023-12945-y] [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: 08/08/2023] [Revised: 10/17/2023] [Accepted: 10/24/2023] [Indexed: 01/12/2024]
Abstract
Infection and invasion are the prerequisites for developing the disease symptoms in a host. While the probable mechanism of host invasion and pathogenesis is known in many pathogens, very little information is available on Leptospira invasion/pathogenesis. For causing systemic infection Leptospira must transmigrate across epithelial barriers, which is the most critical and challenging step. Extracellular and membrane-bound proteases play a crucial role in the invasion process. An extensive search for the proteins experimentally proven to be involved in the invasion process through cell junction cleavage in other pathogens has resulted in identifying 26 proteins. The similarity searches on the Leptospira genome for counterparts of these 26 pathogenesis-related proteins identified at least 12 probable coding sequences. The proteins were either extracellular or membrane-bound with a proteolytic domain to cleave the cell junction proteins. This review will emphasize our current understanding of the pathogenic aspects of host cell junction-pathogenic protein interactions involved in the invasion process. Further, potential candidate proteins with cell junction cleavage properties that may be exploited in the diagnostic/therapeutic aspects of leptospirosis will also be discussed. KEY POINTS: • The review focussed on the cell junction cleavage proteins in bacterial pathogenesis • Cell junction disruptors from Leptospira genome are identified using bioinformatics • The review provides insights into the therapeutic/diagnostic interventions possible.
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Affiliation(s)
- Preeti Kumari
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Suhani Yadav
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Sresha Sarkar
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Padikara K Satheeshkumar
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India.
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Nguyen PT, Harris BJ, Mateos DL, González AH, Murray AM, Yarov-Yarovoy V. Structural modeling of ion channels using AlphaFold2, RoseTTAFold2, and ESMFold. Channels (Austin) 2024; 18:2325032. [PMID: 38445990 PMCID: PMC10936637 DOI: 10.1080/19336950.2024.2325032] [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: 09/05/2023] [Accepted: 01/14/2024] [Indexed: 03/07/2024] Open
Abstract
Ion channels play key roles in human physiology and are important targets in drug discovery. The atomic-scale structures of ion channels provide invaluable insights into a fundamental understanding of the molecular mechanisms of channel gating and modulation. Recent breakthroughs in deep learning-based computational methods, such as AlphaFold, RoseTTAFold, and ESMFold have transformed research in protein structure prediction and design. We review the application of AlphaFold, RoseTTAFold, and ESMFold to structural modeling of ion channels using representative voltage-gated ion channels, including human voltage-gated sodium (NaV) channel - NaV1.8, human voltage-gated calcium (CaV) channel - CaV1.1, and human voltage-gated potassium (KV) channel - KV1.3. We compared AlphaFold, RoseTTAFold, and ESMFold structural models of NaV1.8, CaV1.1, and KV1.3 with corresponding cryo-EM structures to assess details of their similarities and differences. Our findings shed light on the strengths and limitations of the current state-of-the-art deep learning-based computational methods for modeling ion channel structures, offering valuable insights to guide their future applications for ion channel research.
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Affiliation(s)
- Phuong Tran Nguyen
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA, USA
| | - Brandon John Harris
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA, USA
- Biophysics Graduate Group, University of California School of Medicine, Davis, CA, USA
| | - Diego Lopez Mateos
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA, USA
- Biophysics Graduate Group, University of California School of Medicine, Davis, CA, USA
| | - Adriana Hernández González
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA, USA
- Biophysics Graduate Group, University of California School of Medicine, Davis, CA, USA
| | | | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA, USA
- Department of Anesthesiology and Pain Medicine, University of California School of Medicine, Davis, CA, USA
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Uehara K, Oshiro E, Ochiai A, Takagi R, Yamato M, Kato A. Lessons learned from contamination with endotoxin originated from the supplement in the cell culture medium. Regen Ther 2024; 27:230-233. [PMID: 38596824 PMCID: PMC11002528 DOI: 10.1016/j.reth.2024.03.022] [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: 01/16/2024] [Revised: 03/13/2024] [Accepted: 03/20/2024] [Indexed: 04/11/2024] Open
Abstract
Introduction Endotoxin is a typical pyrogen derived from the outer membrane of Gram-negative bacteria. In fabricating cell-based medicinal products, it is necessary to control endotoxin in the process and the products. In the quality control tests of our clinical study, endotoxin concentration in the culture supernatant of autologous oral mucosal epithelial cell sheets exceeded the criterion value. Therefore, endotoxin measurements were conducted to clarify the cause of the endotoxin contamination. Methods The reagents used to prepare the culture medium, the unused culture medium, and the culture supernatants were diluted with pure water. Endotoxin concentrations in the diluted samples were measured. Results Endotoxin was detected in both the unused culture medium and the culture supernatant of the epithelial cell sheets at higher concentrations than the criterion value. Therefore, endotoxin concentrations in the reagents used to prepare the culture medium were measured and were found to be below the criterion value, except for cholera toxin. On the other hand, three lots of cholera toxin products were used for the measurement, and the endotoxin concentrations were higher than the criterion value. The results indicate that the endotoxin contamination is caused by the cholera toxin product. Conclusions To prevent endotoxin contamination in cell-based medicinal products, endotoxin concentrations in reagents used for the fabrication should be measured in the facility conducting clinical research or confirmed by an adequate certificate of analysis from the manufacturers of the reagents.
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Affiliation(s)
- Koaki Uehara
- Social Medical Corporation Yuuaikai, Yuuai Medical Center, Advanced Medical Research Center, 50-5, Yone, Tomigusuku-shi, Okinawa 901-0224, Japan
| | - Eriko Oshiro
- Social Medical Corporation Yuuaikai, Yuuai Medical Center, Advanced Medical Research Center, 50-5, Yone, Tomigusuku-shi, Okinawa 901-0224, Japan
| | - Atsushi Ochiai
- Social Medical Corporation Yuuaikai, Yuuai Medical Center, Advanced Medical Research Center, 50-5, Yone, Tomigusuku-shi, Okinawa 901-0224, Japan
| | - Ryo Takagi
- Institute of Advanced Biomedical Engineering and Science, Tokyo Women's Medical University, TWIns, 8-1 Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Masayuki Yamato
- Institute of Advanced Biomedical Engineering and Science, Tokyo Women's Medical University, TWIns, 8-1 Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Atsunaga Kato
- Social Medical Corporation Yuuaikai, Yuuai Medical Center, Advanced Medical Research Center, 50-5, Yone, Tomigusuku-shi, Okinawa 901-0224, Japan
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Kembou-Ringert JE, Hotio FN, Steinhagen D, Thompson KD, Surachetpong W, Rakus K, Daly JM, Goonawardane N, Adamek M. Knowns and unknowns of TiLV-associated neuronal disease. Virulence 2024; 15:2329568. [PMID: 38555518 PMCID: PMC10984141 DOI: 10.1080/21505594.2024.2329568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/07/2024] [Indexed: 04/02/2024] Open
Abstract
Tilapia Lake Virus (TiLV) is associated with pathological changes in the brain of infected fish, but the mechanisms driving the virus's neuropathogenesis remain poorly characterized. TiLV establishes a persistent infection in the brain of infected fish even when the virus is no longer detectable in the peripheral organs, rendering therapeutic interventions and disease management challenging. Moreover, the persistence of the virus in the brain may pose a risk for viral reinfection and spread and contribute to ongoing tissue damage and neuroinflammatory processes. In this review, we explore TiLV-associated neurological disease. We discuss the possible mechanism(s) used by TiLV to enter the central nervous system (CNS) and examine TiLV-induced neuroinflammation and brain immune responses. Lastly, we discuss future research questions and knowledge gaps to be addressed to significantly advance this field.
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Affiliation(s)
- Japhette E. Kembou-Ringert
- Department of infection, immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Fortune N. Hotio
- Department of Animal Biology, Faculty of Science, University of Dschang, Dschang, Cameroon
| | - Dieter Steinhagen
- Fish Disease Research Unit, Institute for parasitology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Kim D. Thompson
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, UK
| | - Win Surachetpong
- Department of Veterinary Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Krzysztof Rakus
- Department of Evolutionary Immunology, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Janet M. Daly
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
| | - Niluka Goonawardane
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Mikolaj Adamek
- Fish Disease Research Unit, Institute for parasitology, University of Veterinary Medicine Hannover, Hannover, Germany
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Perales IE, Jones SD, Piaszynski KM, Geyer PK. Developmental changes in nuclear lamina components during germ cell differentiation. Nucleus 2024; 15:2339214. [PMID: 38597409 PMCID: PMC11008544 DOI: 10.1080/19491034.2024.2339214] [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: 02/20/2024] [Accepted: 04/02/2024] [Indexed: 04/11/2024] Open
Abstract
The nuclear lamina (NL) changes composition for regulation of nuclear events. We investigated changes that occur in Drosophila oogenesis, revealing switches in NL composition during germ cell differentiation. Germline stem cells (GSCs) express only LamB and predominantly emerin, whereas differentiating nurse cells predominantly express LamC and emerin2. A change in LamC-specific localization also occurs, wherein phosphorylated LamC redistributes to the nuclear interior only in the oocyte, prior to transcriptional reactivation of the meiotic genome. These changes support existing concepts that LamC promotes differentiation, a premise that was tested. Remarkably ectopic LamC production in GSCs did not promote premature differentiation. Increased LamC levels in differentiating germ cells altered internal nuclear structure, increased RNA production, and reduced female fertility due to defects in eggshell formation. These studies suggest differences between Drosophila lamins are regulatory, not functional, and reveal an unexpected robustness to level changes of a major scaffolding component of the NL.
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Affiliation(s)
- Isabella E. Perales
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, IA, USA
| | - Samuel D. Jones
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, IA, USA
| | | | - Pamela K. Geyer
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, IA, USA
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Attar AG, Paturej J, Banigan EJ, Erbaş A. Chromatin phase separation and nuclear shape fluctuations are correlated in a polymer model of the nucleus. Nucleus 2024; 15:2351957. [PMID: 38753956 DOI: 10.1080/19491034.2024.2351957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/28/2024] [Indexed: 05/18/2024] Open
Abstract
Abnormal cell nuclear shapes are hallmarks of diseases, including progeria, muscular dystrophy, and many cancers. Experiments have shown that disruption of heterochromatin and increases in euchromatin lead to nuclear deformations, such as blebs and ruptures. However, the physical mechanisms through which chromatin governs nuclear shape are poorly understood. To investigate how heterochromatin and euchromatin might govern nuclear morphology, we studied chromatin microphase separation in a composite coarse-grained polymer and elastic shell simulation model. By varying chromatin density, heterochromatin composition, and heterochromatin-lamina interactions, we show how the chromatin phase organization may perturb nuclear shape. Increasing chromatin density stabilizes the lamina against large fluctuations. However, increasing heterochromatin levels or heterochromatin-lamina interactions enhances nuclear shape fluctuations by a "wetting"-like interaction. In contrast, fluctuations are insensitive to heterochromatin's internal structure. Our simulations suggest that peripheral heterochromatin accumulation could perturb nuclear morphology, while nuclear shape stabilization likely occurs through mechanisms other than chromatin microphase organization.
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Affiliation(s)
- Ali Goktug Attar
- UNAM-National Nanotechnology Research Center and Institute of Materials Science & Nanotechnology, Bilkent University, Ankara, Turkey
| | | | - Edward J Banigan
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Aykut Erbaş
- UNAM-National Nanotechnology Research Center and Institute of Materials Science & Nanotechnology, Bilkent University, Ankara, Turkey
- Institute of Physics, University of Silesia, Chorzów, Poland
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Wu Y, Zhao Y, Guan Z, Esmaeili S, Xiao Z, Kuriakose D. JNK3 inhibitors as promising pharmaceuticals with neuroprotective properties. Cell Adh Migr 2024; 18:1-11. [PMID: 38357988 PMCID: PMC10878020 DOI: 10.1080/19336918.2024.2316576] [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: 02/06/2024] [Indexed: 02/16/2024] Open
Abstract
The intensive study and investigation of neuroprotective therapy for central nervous system (CNS) diseases is ongoing. Due to shared mechanisms of neurodegeneration, a neuroprotective approach might offer benefits across multiple neurological disorders, despite variations in symptoms or injuries. C-Jun N-terminal Kinase 3 (JNK3) is found primarily in the CNS and is involved in physiological processes such as brain development, synapse formation, and memory formation. The potential of JNK3 as a target for pharmacological development holds promise for advancing neuroprotective therapies. Developing small molecule JNK3 inhibitors into drugs with neuroprotective qualities could facilitate neuronal restoration and self-repair. This review focuses on elucidating key neuroprotective mechanisms, exploring the interplay between neurodegenerative diseases and neuroprotection, and discussing advancements in JNK3 inhibitor drug development.
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Affiliation(s)
- Yibeini Wu
- Department of Anatomy and Developmental biology, Monash University, Clayton, Vic, Australia
| | - Yiling Zhao
- Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Ziman Guan
- Department of Anatomy and Developmental biology, Monash University, Clayton, Vic, Australia
| | - Sajjad Esmaeili
- Department of Anatomy and Developmental biology, Monash University, Clayton, Vic, Australia
| | - Zhicheng Xiao
- Department of Anatomy and Developmental biology, Monash University, Clayton, Vic, Australia
- Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Diji Kuriakose
- Department of Anatomy and Developmental biology, Monash University, Clayton, Vic, Australia
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Krushkal J, Zhao Y, Roney K, Zhu W, Brooks A, Wilsker D, Parchment RE, McShane LM, Doroshow JH. Association of changes in expression of HDAC and SIRT genes after drug treatment with cancer cell line sensitivity to kinase inhibitors. Epigenetics 2024; 19:2309824. [PMID: 38369747 PMCID: PMC10878021 DOI: 10.1080/15592294.2024.2309824] [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: 07/24/2023] [Accepted: 01/14/2024] [Indexed: 02/20/2024] Open
Abstract
Histone deacetylases (HDACs) and sirtuins (SIRTs) are important epigenetic regulators of cancer pathways. There is a limited understanding of how transcriptional regulation of their genes is affected by chemotherapeutic agents, and how such transcriptional changes affect tumour sensitivity to drug treatment. We investigated the concerted transcriptional response of HDAC and SIRT genes to 15 approved antitumor agents in the NCI-60 cancer cell line panel. Antitumor agents with diverse mechanisms of action induced upregulation or downregulation of multiple HDAC and SIRT genes. HDAC5 was upregulated by dasatinib and erlotinib in the majority of the cell lines. Tumour cell line sensitivity to kinase inhibitors was associated with upregulation of HDAC5, HDAC1, and several SIRT genes. We confirmed changes in HDAC and SIRT expression in independent datasets. We also experimentally validated the upregulation of HDAC5 mRNA and protein expression by dasatinib in the highly sensitive IGROV1 cell line. HDAC5 was not upregulated in the UACC-257 cell line resistant to dasatinib. The effects of cancer drug treatment on expression of HDAC and SIRT genes may influence chemosensitivity and may need to be considered during chemotherapy.
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Affiliation(s)
- Julia Krushkal
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - Yingdong Zhao
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - Kyle Roney
- Department of Biostatistics and Bioinformatics, George Washington University, Washington, DC, USA
| | - Weimin Zhu
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Alan Brooks
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Deborah Wilsker
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ralph E. Parchment
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lisa M. McShane
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - James H. Doroshow
- Division of Cancer Treatment and Diagnosis and Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
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Ng XY, Cao M. Dysfunction of synaptic endocytic trafficking in Parkinson's disease. Neural Regen Res 2024; 19:2649-2660. [PMID: 38595283 PMCID: PMC11168511 DOI: 10.4103/nrr.nrr-d-23-01624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/12/2023] [Accepted: 01/03/2024] [Indexed: 04/11/2024] Open
Abstract
Parkinson's disease is characterized by the selective degeneration of dopamine neurons in the nigrostriatal pathway and dopamine deficiency in the striatum. The precise reasons behind the specific degeneration of these dopamine neurons remain largely elusive. Genetic investigations have identified over 20 causative PARK genes and 90 genomic risk loci associated with both familial and sporadic Parkinson's disease. Notably, several of these genes are linked to the synaptic vesicle recycling process, particularly the clathrin-mediated endocytosis pathway. This suggests that impaired synaptic vesicle recycling might represent an early feature of Parkinson's disease, followed by axonal degeneration and the eventual loss of dopamine cell bodies in the midbrain via a "dying back" mechanism. Recently, several new animal and cellular models with Parkinson's disease-linked mutations affecting the endocytic pathway have been created and extensively characterized. These models faithfully recapitulate certain Parkinson's disease-like features at the animal, circuit, and cellular levels, and exhibit defects in synaptic membrane trafficking, further supporting the findings from human genetics and clinical studies. In this review, we will first summarize the cellular and molecular findings from the models of two Parkinson's disease-linked clathrin uncoating proteins: auxilin (DNAJC6/PARK19) and synaptojanin 1 (SYNJ1/PARK20). The mouse models carrying these two PARK gene mutations phenocopy each other with specific dopamine terminal pathology and display a potent synergistic effect. Subsequently, we will delve into the involvement of several clathrin-mediated endocytosis-related proteins (GAK, endophilin A1, SAC2/INPP5F, synaptotagmin-11), identified as Parkinson's disease risk factors through genome-wide association studies, in Parkinson's disease pathogenesis. We will also explore the direct or indirect roles of some common Parkinson's disease-linked proteins (alpha-synuclein (PARK1/4), Parkin (PARK2), and LRRK2 (PARK8)) in synaptic endocytic trafficking. Additionally, we will discuss the emerging novel functions of these endocytic proteins in downstream membrane traffic pathways, particularly autophagy. Given that synaptic dysfunction is considered as an early event in Parkinson's disease, a deeper understanding of the cellular mechanisms underlying synaptic vesicle endocytic trafficking may unveil novel targets for early diagnosis and the development of interventional therapies for Parkinson's disease. Future research should aim to elucidate why generalized synaptic endocytic dysfunction leads to the selective degeneration of nigrostriatal dopamine neurons in Parkinson's disease.
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Affiliation(s)
- Xin Yi Ng
- Programme in Neuroscience and Behavioural Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Mian Cao
- Programme in Neuroscience and Behavioural Disorders, Duke-NUS Medical School, Singapore, Singapore
- Department of Physiology, National University of Singapore, Singapore, Singapore
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Wang S, Qi X, Liu D, Xie D, Jiang B, Wang J, Wang X, Wu G. The implications for urological malignancies of non-coding RNAs in the the tumor microenvironment. Comput Struct Biotechnol J 2024; 23:491-505. [PMID: 38249783 PMCID: PMC10796827 DOI: 10.1016/j.csbj.2023.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/08/2023] [Accepted: 12/16/2023] [Indexed: 01/23/2024] Open
Abstract
Urological malignancies are a major global health issue because of their complexity and the wide range of ways they affect patients. There's a growing need for in-depth research into these cancers, especially at the molecular level. Recent studies have highlighted the importance of non-coding RNAs (ncRNAs) – these don't code for proteins but are crucial in controlling genes – and the tumor microenvironment (TME), which is no longer seen as just a background factor but as an active player in cancer progression. Understanding how ncRNAs and the TME interact is key for finding new ways to diagnose and predict outcomes in urological cancers, and for developing new treatments. This article reviews the basic features of ncRNAs and goes into detail about their various roles in the TME, focusing specifically on how different ncRNAs function and act in urological malignancies.
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Affiliation(s)
- Shijin Wang
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Xiaochen Qi
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Dequan Liu
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Deqian Xie
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Bowen Jiang
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Jin Wang
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Xiaoxi Wang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Guangzhen Wu
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
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Lai J, Zhou Z, Hu K, Yu H, Su X, Niu X, Li H, Mao S. N6-methyladenosine methylation analysis of long noncoding RNAs and mRNAs in 5-FU-resistant colon cancer cells. Epigenetics 2024; 19:2298058. [PMID: 38145548 PMCID: PMC10761136 DOI: 10.1080/15592294.2023.2298058] [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: 07/03/2023] [Accepted: 12/13/2023] [Indexed: 12/27/2023] Open
Abstract
N6 methyladenosine (m6A), methylation at the sixth N atom of adenosine, is the most common and abundant modification in mammalian mRNAs and non-coding RNAs. Increasing evidence shows that the alteration of m6A modification level could regulate tumour proliferation, metastasis, self-renewal, and immune infiltration by regulating the related expression of tumour genes. However, the role of m6A modification in colorectal cancer (CRC) drug resistance is unclear. Here, MeRIP-seq and RNA-seq techniques were utilized to obtain mRNA, lncRNA expression, and their methylation profiles in 5-Fluorouracil (5-FU)-resistant colon cancer HCT-15 cells and control cells. In addition, we performed detailed bioinformatics analysis as well as in vitro experiments of lncRNA to explore the function of lncRNA with differential m6A in CRC progression and drug resistance. In this study, we obtained the m6A methylomic landscape of CRC cells and resistance group cells by MeRIP-seq and RNA-seq. We identified 3698 differential m6A peaks, of which 2224 were hypermethylated, and 1474 were hypomethylated. Among the lncRNAs, 60 were hypermethylated, and 38 were hypomethylated. GO and KEGG analysis annotations showed significant enrichment of endocytosis and MAPK signalling pathways. Moreover, knockdown of lncRNA ADIRF-AS1 and AL139035.1 promoted CRC proliferation and invasive metastasis in vitro. lncRNA- mRNA network showed that ADIRF-AS1 and AL139035.1 May play a key role in regulating drug resistance formation. We provide the first m6A methylation profile in 5-FU resistance CRC cells and analyse the functions of differential m6A-modified mRNAs and lncRNAs. Our results indicated that differential m6A RNAs were significantly associated with MAPK signalling and endocytosis after induction of 5-FU resistance. Knockdown of LncRNA ADIRF-AS1 and AL139035.1 promotes CRC progression and might be critical in regulating drug resistance formation.
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Affiliation(s)
- Jie Lai
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Department of General Surgery, Pingxiang People’s Hospital, Pingxiang, Jiangxi, China
| | - Zhiyong Zhou
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Kan Hu
- Department of General Surgery, Pingxiang People’s Hospital, Pingxiang, Jiangxi, China
| | - HongLong Yu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xingyao Su
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xiaoqiang Niu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Huizi Li
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Shengxun Mao
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
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Li J, Tang Y, Long F, Tian L, Tang A, Ding L, Chen J, Liu M. Integrating bulk RNA-seq and scRNA-seq analyses revealed the function and clinical value of thrombospondins in colon cancer. Comput Struct Biotechnol J 2024; 23:2251-2266. [PMID: 38827236 PMCID: PMC11140486 DOI: 10.1016/j.csbj.2024.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 06/04/2024] Open
Abstract
Background Acting as mediators in cell-matrix and cell-cell communication, matricellular proteins play a crucial role in cancer progression. Thrombospondins (TSPs), a type of matricellular glycoproteins, are key regulators in cancer biology with multifaceted roles. Although TSPs have been implicated in anti-tumor immunity and epithelial-mesenchymal transition (EMT) in several malignancies, their specific roles to colon cancer remain elusive. Addressing this knowledge gap is essential, as understanding the function of TSPs in colon cancer could identify new therapeutic targets and prognostic markers. Methods Analyzing 1981 samples from 10 high-throughput datasets, including six bulk RNA-seq, three scRNA-seq, and one spatial transcriptome dataset, our study investigated the prognostic relevance, risk stratification value, immune heterogeneity, and cellular origin of TSPs, as well as their influence on cancer-associated fibroblasts (CAFs). Utilizing survival analysis, unsupervised clustering, and functional enrichment, along with multiple correlation analyses of the tumor-microenvironment (TME) via Gene Set Variation Analysis (GSVA), spatial localization, Monocle2, and CellPhoneDB, we provided insights into the clinical and cellular implications of TSPs. Results First, we observed significant upregulation of THBS2 and COMP in colon cancer, both of which displayed significant prognostic value. Additionally, we detected a significant positive correlation between TSPs and immune cells, as well as marker genes of EMT. Second, based on TSPs expression, patients were divided into two clusters with distinct prognoses: the high TSPs expression group (TSPs-H) was characterized by pronounced immune and stromal cell infiltration, and notably elevated T-cell exhaustion scores. Subsequently, we found that THBS2 and COMP may be associated with the differentiation of CAFs into pan-iCAFs and pan-dCAFs, which are known for their heightened matrix remodeling activities. Moreover, THBS2 enhanced CAFs communication with vascular endothelial cells and monocyte-macrophages. CAFs expressing THBS2 (THBS2+ CAFs) demonstrated higher scores across multiple signaling pathways, including angiogenic, EMT, Hedgehog, Notch, Wnt, and TGF-β, when compared to THBS2- CAFs. These observations suggest that THBS2 may be associated with stronger pro-carcinogenic activity in CAFs. Conclusions This study revealed the crucial role of TSPs and the significant correlation between THBS2 and CAFs interactions in colon cancer progression, providing valuable insights for targeting TSPs to mitigate cancer progression.
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Affiliation(s)
- Jing Li
- Key Laboratory of Clinical Laboratory Diagnostics, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400046, China
| | - Ying Tang
- Key Laboratory of Clinical Laboratory Diagnostics, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400046, China
- Medical Laboratory, People's Hospital of Qingbaijiang District, Chengdu 61300, China
| | - Fei Long
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
- Center for Single-Cell Omics and Tumor Liquid Biopsy, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Luyao Tian
- Key Laboratory of Clinical Laboratory Diagnostics, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400046, China
| | - Ao Tang
- Key Laboratory of Clinical Laboratory Diagnostics, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400046, China
| | - LiHui Ding
- Key Laboratory of Clinical Laboratory Diagnostics, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400046, China
| | - Juan Chen
- Key Laboratory of Clinical Laboratory Diagnostics, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400046, China
| | - Mingwei Liu
- Key Laboratory of Clinical Laboratory Diagnostics, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400046, China
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Chen JN, Yang XJ, Cong M, Zhu LJ, Wu X, Wang LT, Sha L, Yu Y, He QR, Ding F, Xian H, Shi HY. Promotive effect of skin precursor-derived Schwann cells on brachial plexus neurotomy and motor neuron damage repair through milieu-regulating secretome. Regen Ther 2024; 27:365-380. [PMID: 38694448 PMCID: PMC11061650 DOI: 10.1016/j.reth.2024.04.002] [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: 08/28/2023] [Revised: 04/02/2024] [Accepted: 04/11/2024] [Indexed: 05/04/2024] Open
Abstract
Brachial plexus injury (BPI) with motor neurons (MNs) damage still remain poor recovery in preclinical research and clinical therapy, while cell-based therapy approaches emerged as novel strategies. Previous work of rat skin precursor-derived Schwann cells (SKP-SCs) provided substantial foundation for repairing peripheral nerve injury (PNI). Given that, our present work focused on exploring the repair efficacy and possible mechanisms of SKP-SCs implantation on rat BPI combined with neurorrhaphy post-neurotomy. Results indicated the significant locomotive and sensory function recovery, with improved morphological remodeling of regenerated nerves and angiogenesis, as well as amelioration of target muscles atrophy and motor endplate degeneration. Besides, MNs could restore from oxygen-glucose-deprivation (OGD) injury upon SKP-SCs-sourced secretome treatment, implying the underlying paracrine mechanisms. Moreover, rat cytokine array assay detected 67 cytokines from SKP-SC-secretome, and bioinformatic analyses of screened 32 cytokines presented multiple functional clusters covering diverse cell types, including inflammatory cells, Schwann cells, vascular endothelial cells (VECs), neurons, and SKP-SCs themselves, relating distinct biological processes to nerve regeneration. Especially, a panel of hypoxia-responsive cytokines (HRCK), can participate into multicellular biological process regulation for permissive regeneration milieu, which underscored the benefits of SKP-SCs and sourced secretome, facilitating the chorus of nerve regenerative microenvironment. Furthermore, platelet-derived growth factor-AA (PDGF-AA) and vascular endothelial growth factor-A (VEGF-A) were outstanding cytokines involved with nerve regenerative microenvironment regulating, with significantly elevated mRNA expression level in hypoxia-responsive SKP-SCs. Altogether, through recapitulating the implanted SKP-SCs and derived secretome as niche sensor and paracrine transmitters respectively, HRCK would be further excavated as molecular underpinning of the neural recuperative mechanizations for efficient cell therapy; meanwhile, the analysis paradigm in this study validated and anticipated the actions and mechanisms of SKP-SCs on traumatic BPI repair, and was beneficial to identify promising bioactive molecule cocktail and signaling targets for cell-free therapy strategy on neural repair and regeneration.
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Affiliation(s)
- Jia-nan Chen
- School of Medicine, Nantong University, Nantong, 226001, China
- Department of Pediatric Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Xiao-jia Yang
- School of Medicine, Nantong University, Nantong, 226001, China
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education and Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Meng Cong
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education and Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Ling-jie Zhu
- School of Medicine, Nantong University, Nantong, 226001, China
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education and Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Xia Wu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education and Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Li-ting Wang
- School of Medicine, Nantong University, Nantong, 226001, China
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education and Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Lei Sha
- School of Medicine, Nantong University, Nantong, 226001, China
| | - Yan Yu
- School of Medicine, Nantong University, Nantong, 226001, China
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education and Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Qian-ru He
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education and Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Fei Ding
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education and Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Hua Xian
- School of Medicine, Nantong University, Nantong, 226001, China
- Department of Pediatric Surgery, Affiliated Hospital of Nantong University, Nantong University, Nantong, 226001, China
| | - Hai-yan Shi
- School of Medicine, Nantong University, Nantong, 226001, China
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education and Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
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Zhang X, Sun D, Wong K, Salkini A, Najafi H, Kim WJ. The astrocyte-enriched gene deathstar plays a crucial role in the development, locomotion, and lifespan of D. melanogaster. Fly (Austin) 2024; 18:2368336. [PMID: 38884422 PMCID: PMC11185185 DOI: 10.1080/19336934.2024.2368336] [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: 10/22/2023] [Accepted: 06/11/2024] [Indexed: 06/18/2024] Open
Abstract
The Drosophila melanogaster brain is a complex organ with various cell types, orchestrating the development, physiology, and behaviors of the fly. While each cell type in Drosophila brain is known to express a unique gene set, their complete genetic profile is still unknown. Advances in the RNA sequencing techniques at single-cell resolution facilitate identifying novel cell type markers and/or re-examining the specificity of the available ones. In this study, exploiting a single-cell RNA sequencing data of Drosophila optic lobe, we categorized the cells based on their expression pattern for known markers, then the genes with enriched expression in astrocytes were identified. CG11000 was identified as a gene with a comparable expression profile to the Eaat1 gene, an astrocyte marker, in every individual cell inside the Drosophila optic lobe and midbrain, as well as in the entire Drosophila brain throughout its development. Consistent with our bioinformatics data, immunostaining of the brains dissected from transgenic adult flies showed co-expression of CG11000 with Eaat1 in a set of single cells corresponding to the astrocytes in the Drosophila brain. Physiologically, inhibiting CG11000 through RNA interference disrupted the normal development of male D. melanogaster, while having no impact on females. Expression suppression of CG11000 in adult flies led to decreased locomotion activity and also shortened lifespan specifically in astrocytes, indicating the gene's significance in astrocytes. We designated this gene as 'deathstar' due to its crucial role in maintaining the star-like shape of glial cells, astrocytes, throughout their development into adult stage.
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Affiliation(s)
- Xiaoli Zhang
- The HIT Center for Life Sciences, Harbin Institute of Technology, Harbin, China
| | - Dongyu Sun
- The HIT Center for Life Sciences, Harbin Institute of Technology, Harbin, China
| | - Kyle Wong
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Ammar Salkini
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Hadi Najafi
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Woo Jae Kim
- The HIT Center for Life Sciences, Harbin Institute of Technology, Harbin, China
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
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Hao P, Yang Z, So KF, Li X. A core scientific problem in the treatment of central nervous system diseases: newborn neurons. Neural Regen Res 2024; 19:2588-2601. [PMID: 38595278 PMCID: PMC11168522 DOI: 10.4103/nrr.nrr-d-23-01775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/06/2024] [Accepted: 02/22/2024] [Indexed: 04/11/2024] Open
Abstract
It has long been asserted that failure to recover from central nervous system diseases is due to the system's intricate structure and the regenerative incapacity of adult neurons. Yet over recent decades, numerous studies have established that endogenous neurogenesis occurs in the adult central nervous system, including humans'. This has challenged the long-held scientific consensus that the number of adult neurons remains constant, and that new central nervous system neurons cannot be created or renewed. Herein, we present a comprehensive overview of the alterations and regulatory mechanisms of endogenous neurogenesis following central nervous system injury, and describe novel treatment strategies that target endogenous neurogenesis and newborn neurons in the treatment of central nervous system injury. Central nervous system injury frequently results in alterations of endogenous neurogenesis, encompassing the activation, proliferation, ectopic migration, differentiation, and functional integration of endogenous neural stem cells. Because of the unfavorable local microenvironment, most activated neural stem cells differentiate into glial cells rather than neurons. Consequently, the injury-induced endogenous neurogenesis response is inadequate for repairing impaired neural function. Scientists have attempted to enhance endogenous neurogenesis using various strategies, including using neurotrophic factors, bioactive materials, and cell reprogramming techniques. Used alone or in combination, these therapeutic strategies can promote targeted migration of neural stem cells to an injured area, ensure their survival and differentiation into mature functional neurons, and facilitate their integration into the neural circuit. Thus can integration replenish lost neurons after central nervous system injury, by improving the local microenvironment. By regulating each phase of endogenous neurogenesis, endogenous neural stem cells can be harnessed to promote effective regeneration of newborn neurons. This offers a novel approach for treating central nervous system injury.
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Affiliation(s)
- Peng Hao
- Department of Neurobiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Zhaoyang Yang
- Department of Neurobiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Kwok-Fai So
- Guangdong-HongKong-Macau Institute of CNS Regeneration, Ministry of Education CNS Regeneration Collaborative Joint Laboratory, Jinan University, Guangzhou, Guangdong Province, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong Province, China
- Department of Ophthalmology and State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong Special Administration Region, China
- Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong-Macao Greater Bay Area, Guangzhou, Guangdong Province, China
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Xiaoguang Li
- Department of Neurobiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
- Department of Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
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Chou AA, Lin CH, Chang YC, Chang HW, Lin YC, Pi CC, Kan YM, Chuang HF, Chen HW. Antiviral activity of Vigna radiata extract against feline coronavirus in vitro. Vet Q 2024; 44:1-13. [PMID: 38712855 PMCID: PMC11078076 DOI: 10.1080/01652176.2024.2349665] [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: 04/25/2024] [Indexed: 05/08/2024] Open
Abstract
Feline infectious peritonitis (FIP) is a fatal illness caused by a mutated feline coronavirus (FCoV). This disease is characterized by its complexity, resulting from systemic infection, antibody-dependent enhancement (ADE), and challenges in accessing effective therapeutics. Extract derived from Vigna radiata (L.) R. Wilczek (VRE) exhibits various pharmacological effects, including antiviral activity. This study aimed to investigate the antiviral potential of VRE against FCoV, addressing the urgent need to advance the treatment of FIP. We explored the anti-FCoV activity, antiviral mechanism, and combinational application of VRE by means of in vitro antiviral assays. Our findings reveal that VRE effectively inhibited the cytopathic effect induced by FCoV, reduced viral proliferation, and downregulated spike protein expression. Moreover, VRE blocked FCoV in the early and late infection stages and was effective under in vitro ADE infection. Notably, when combined with VRE, the polymerase inhibitor GS-441524 or protease inhibitor GC376 suppressed FCoV more effectively than monotherapy. In conclusion, this study characterizes the antiviral property of VRE against FCoV in vitro, and VRE possesses therapeutic potential for FCoV treatment.
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Affiliation(s)
- Ai-Ai Chou
- Department of Veterinary Medicine, National Taiwan University, Taipei, Taiwan
| | - Chung-Hui Lin
- National Taiwan University Veterinary Hospital, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Veterinary Clinical Sciences, School of Veterinary Medicine, National Taiwan University, Taipei, Taiwan
- TACS-alliance Research Center, Taipei, Taiwan
| | - Yen-Chen Chang
- Graduate Institute of Molecular and Comparative Pathobiology, School of Veterinary Medicine, National Taiwan University, Taipei, Taiwan
| | - Hui-Wen Chang
- Graduate Institute of Molecular and Comparative Pathobiology, School of Veterinary Medicine, National Taiwan University, Taipei, Taiwan
| | - Yi-Chen Lin
- King’s Ground Biotech Co., Ltd., Pingtung, Taiwan
| | - Chia-Chen Pi
- King’s Ground Biotech Co., Ltd., Pingtung, Taiwan
| | - Yao-Ming Kan
- Department of Veterinary Medicine, National Taiwan University, Taipei, Taiwan
| | - Hao-Fen Chuang
- Department of Veterinary Medicine, National Taiwan University, Taipei, Taiwan
| | - Hui-Wen Chen
- Department of Veterinary Medicine, National Taiwan University, Taipei, Taiwan
- Animal Resource Center, National Taiwan University, Taipei, Taiwan
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Li C, Xiao Y, Kong J, Lai C, Chen Z, Li Z, Xie W. Elucidating the role of MICAL1 in pan-cancer using integrated bioinformatics and experimental approaches. Cell Adh Migr 2024; 18:1-17. [PMID: 38555517 PMCID: PMC10984120 DOI: 10.1080/19336918.2024.2335682] [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: 07/28/2023] [Accepted: 03/22/2024] [Indexed: 04/02/2024] Open
Abstract
Molecule interacting with CasL 1 (MICAL1) is a crucial protein involved in cell motility, axon guidance, cytoskeletal dynamics, and gene transcription. This pan-cancer study analyzed MICAL1 across 33 cancer types using bioinformatics and experiments. Dysregulated expression, diagnostic potential, and prognostic value were assessed. Associations with tumor characteristics, immune factors, and drug sensitivity were explored. Enrichment analysis revealed MICAL1's involvement in metastasis, angiogenesis, metabolism, and immune pathways. Functional experiments demonstrated its impact on renal carcinoma cells. These findings position MICAL1 as a potential biomarker and therapeutic target in specific cancers, warranting further investigation into its role in cancer pathogenesis.
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Affiliation(s)
- Canxuan Li
- Department of Urology, Shenshan Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Shanwei, Guangdong, P. R. China
| | - Yunfei Xiao
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Clinical Research Center for Urological Diseases, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
| | - Jianqiu Kong
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Clinical Research Center for Urological Diseases, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
| | - Cong Lai
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Clinical Research Center for Urological Diseases, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
| | - Zhiliang Chen
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Clinical Research Center for Urological Diseases, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
| | - Zhuohang Li
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Clinical Research Center for Urological Diseases, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
| | - Weibin Xie
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Clinical Research Center for Urological Diseases, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
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Dean WF, Albert RM, Nawara TJ, Ubil M, Beggs RR, Mattheyses AL. Dsg2 ectodomain organization increases throughout desmosome assembly. Cell Adh Migr 2024; 18:1-13. [PMID: 38566311 PMCID: PMC10993919 DOI: 10.1080/19336918.2024.2333366] [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: 04/25/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
Desmosomes are intercellular junctions that regulate mechanical integrity in epithelia and cardiac muscle. Dynamic desmosome remodeling is essential for wound healing and development, yet the mechanisms governing junction assembly remain elusive. While we and others have shown that cadherin ectodomains are highly organized, how this ordered architecture emerges during assembly is unknown. Using fluorescence polarization microscopy, we show that desmoglein 2 (Dsg2) ectodomain order gradually increases during 8 h of assembly, coinciding with increasing adhesive strength. In a scratch wound assay, we observed a similar increase in order in desmosomes assembling at the leading edge of migratory cells. Together, our findings indicate that cadherin organization is a hallmark of desmosome maturity and may play a role in conferring adhesive strength.
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Affiliation(s)
- William F. Dean
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rose M. Albert
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tomasz J. Nawara
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Melanie Ubil
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Reena R. Beggs
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alexa L. Mattheyses
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
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50
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Manaithiya A, Bhowmik R, Acharjee S, Sharma S, Kumar S, Imran M, Mathew B, Parkkila S, Aspatwar A. Elucidating molecular mechanism and chemical space of chalcones through biological networks and machine learning approaches. Comput Struct Biotechnol J 2024; 23:2811-2836. [PMID: 39045026 PMCID: PMC11263914 DOI: 10.1016/j.csbj.2024.07.006] [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: 05/09/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/25/2024] Open
Abstract
We developed a bio-cheminformatics method, exploring disease inhibition mechanisms using machine learning-enhanced quantitative structure-activity relationship (ML-QSAR) models and knowledge-driven neural networks. ML-QSAR models were developed using molecular fingerprint descriptors and the Random Forest algorithm to explore the chemical spaces of Chalcones inhibitors against diverse disease properties, including antifungal, anti-inflammatory, anticancer, antimicrobial, and antiviral effects. We generated and validated robust machine learning-based bioactivity prediction models (https://github.com/RatulChemoinformatics/QSAR) for the top genes. These models underwent ROC and applicability domain analysis, followed by molecular docking studies to elucidate the molecular mechanisms of the molecules. Through comprehensive neural network analysis, crucial genes such as AKT1, HSP90AA1, SRC, and STAT3 were identified. The PubChem fingerprint-based model revealed key descriptors: PubchemFP521 for AKT1, PubchemFP180 for SRC, PubchemFP633 for HSP90AA1, and PubchemFP145 and PubchemFP338 for STAT3, consistently contributing to bioactivity across targets. Notably, chalcone derivatives demonstrated significant bioactivity against target genes, with compound RA1 displaying a predictive pIC50 value of 5.76 against HSP90AA1 and strong binding affinities across other targets. Compounds RA5 to RA7 also exhibited high binding affinity scores comparable to or exceeding existing drugs. These findings emphasize the importance of knowledge-based neural network-based research for developing effective drugs against diverse disease properties. These interactions warrant further in vitro and in vivo investigations to elucidate their potential in rational drug design. The presented models provide valuable insights for inhibitor design and hold promise for drug development. Future research will prioritize investigating these molecules for mycobacterium tuberculosis, enhancing the comprehension of effectiveness in addressing infectious diseases.
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Affiliation(s)
- Ajay Manaithiya
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Ratul Bhowmik
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Satarupa Acharjee
- Department of Pharmacy, NSHM Knowledge Campus, Kolkata-Group of Institutions, Kolkata, West Bengal 700053, India
| | - Sameer Sharma
- Department of Bioinformatics, BioNome, Bangalore 560043, India
| | - Sunil Kumar
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS, Health Sciences Campus, Kochi, India
| | - Mohd. Imran
- Department of Pharmaceutical Chemistry, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Bijo Mathew
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS, Health Sciences Campus, Kochi, India
| | - Seppo Parkkila
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Ltd., Tampere University Hospital, Tampere, Finland
| | - Ashok Aspatwar
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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