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Wu Y, Shao W, Yan M, Wang Y, Xu P, Huang G, Li X, Gregory BD, Yang J, Wang H, Yu X. Transfer learning enables identification of multiple types of RNA modifications using nanopore direct RNA sequencing. Nat Commun 2024; 15:4049. [PMID: 38744925 PMCID: PMC11094168 DOI: 10.1038/s41467-024-48437-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 04/26/2024] [Indexed: 05/16/2024] Open
Abstract
Nanopore direct RNA sequencing (DRS) has emerged as a powerful tool for RNA modification identification. However, concurrently detecting multiple types of modifications in a single DRS sample remains a challenge. Here, we develop TandemMod, a transferable deep learning framework capable of detecting multiple types of RNA modifications in single DRS data. To train high-performance TandemMod models, we generate in vitro epitranscriptome datasets from cDNA libraries, containing thousands of transcripts labeled with various types of RNA modifications. We validate the performance of TandemMod on both in vitro transcripts and in vivo human cell lines, confirming its high accuracy for profiling m6A and m5C modification sites. Furthermore, we perform transfer learning for identifying other modifications such as m7G, Ψ, and inosine, significantly reducing training data size and running time without compromising performance. Finally, we apply TandemMod to identify 3 types of RNA modifications in rice grown in different environments, demonstrating its applicability across species and conditions. In summary, we provide a resource with ground-truth labels that can serve as benchmark datasets for nanopore-based modification identification methods, and TandemMod for identifying diverse RNA modifications using a single DRS sample.
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Affiliation(s)
- You Wu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenna Shao
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mengxiao Yan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yuqin Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Pengfei Xu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Guoqiang Huang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaofei Li
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
- Chenshan Scientific Research Center of CAS Center for Excellence in Molecular Plant Sciences, Shanghai, 201602, China.
| | - Hongxia Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
- Chenshan Scientific Research Center of CAS Center for Excellence in Molecular Plant Sciences, Shanghai, 201602, China.
| | - Xiang Yu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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2
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Peng Q, Liu X, Li W, Jing H, Li J, Gao X, Luo Q, Breeze CE, Pan S, Zheng Q, Li G, Qian J, Yuan L, Yuan N, You C, Du S, Zheng Y, Yuan Z, Tan J, Jia P, Wang J, Zhang G, Lu X, Shi L, Guo S, Liu Y, Ni T, Wen B, Zeng C, Jin L, Teschendorff AE, Liu F, Wang S. Analysis of blood methylation quantitative trait loci in East Asians reveals ancestry-specific impacts on complex traits. Nat Genet 2024; 56:846-860. [PMID: 38641644 DOI: 10.1038/s41588-023-01494-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 08/02/2023] [Indexed: 04/21/2024]
Abstract
Methylation quantitative trait loci (mQTLs) are essential for understanding the role of DNA methylation changes in genetic predisposition, yet they have not been fully characterized in East Asians (EAs). Here we identified mQTLs in whole blood from 3,523 Chinese individuals and replicated them in additional 1,858 Chinese individuals from two cohorts. Over 9% of mQTLs displayed specificity to EAs, facilitating the fine-mapping of EA-specific genetic associations, as shown for variants associated with height. Trans-mQTL hotspots revealed biological pathways contributing to EA-specific genetic associations, including an ERG-mediated 233 trans-mCpG network, implicated in hematopoietic cell differentiation, which likely reflects binding efficiency modulation of the ERG protein complex. More than 90% of mQTLs were shared between different blood cell lineages, with a smaller fraction of lineage-specific mQTLs displaying preferential hypomethylation in the respective lineages. Our study provides new insights into the mQTL landscape across genetic ancestries and their downstream effects on cellular processes and diseases/traits.
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Affiliation(s)
- Qianqian Peng
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xinxuan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Wenran Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Han Jing
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jiarui Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xingjian Gao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Qi Luo
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | - Siyu Pan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Qiwen Zheng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Guochao Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Jiaqiang Qian
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Liyun Yuan
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Na Yuan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Chenglong You
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Siyuan Du
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, and Human Phenome Institute, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Ziyu Yuan
- Taizhou Institute of Health Sciences, Fudan University, Taizhou, China
| | - Jingze Tan
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Peilin Jia
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, and Human Phenome Institute, Fudan University, Shanghai, China
- Taizhou Institute of Health Sciences, Fudan University, Taizhou, China
- Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai, China
| | - Guoqing Zhang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Taizhou Institute of Health Sciences, Fudan University, Taizhou, China
| | - Xianping Lu
- Shenzhen Chipscreen Biosciences Co. Ltd., Shenzhen, China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, and Human Phenome Institute, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
- Taizhou Institute of Health Sciences, Fudan University, Taizhou, China
| | - Shicheng Guo
- Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Yun Liu
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Bo Wen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, and Human Phenome Institute, Fudan University, Shanghai, China
- The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Changqing Zeng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, and Human Phenome Institute, Fudan University, Shanghai, China
- Taizhou Institute of Health Sciences, Fudan University, Taizhou, China
- Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai, China
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Fan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China.
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, Kingdom of Saudi Arabia.
| | - Sijia Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- Taizhou Institute of Health Sciences, Fudan University, Taizhou, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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3
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Shang CF, Wang YF, Zhao MT, Fan QX, Zhao S, Qian Y, Xu SJ, Mu Y, Hao J, Du JL. Real-time analysis of large-scale neuronal imaging enables closed-loop investigation of neural dynamics. Nat Neurosci 2024; 27:1014-1018. [PMID: 38467902 DOI: 10.1038/s41593-024-01595-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 02/07/2024] [Indexed: 03/13/2024]
Abstract
Large-scale imaging of neuronal activities is crucial for understanding brain functions. However, it is challenging to analyze large-scale imaging data in real time, preventing closed-loop investigation of neural circuitry. Here we develop a real-time analysis system with a field programmable gate array-graphics processing unit design for an up to 500-megabyte-per-second image stream. Adapted to whole-brain imaging of awake larval zebrafish, the system timely extracts activity from up to 100,000 neurons and enables closed-loop perturbations of neural dynamics.
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Affiliation(s)
- Chun-Feng Shang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- Guangdong-Hongkong-Macau Institute of CNS Regeneration, Ministry of Education CNS Regeneration Collaborative Joint Laboratory, Jinan University, Guangzhou, China
- Shenzhen Institute of Neuroscience, Shenzhen, China
| | - Yu-Fan Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mei-Ting Zhao
- Institute of Automation, Chinese Academy of Sciences, Beijing, China
- Guangdong Institute of Artificial Intelligence and Advanced Computing, Guangzhou, China
| | - Qiu-Xiang Fan
- Institute of Automation, Chinese Academy of Sciences, Beijing, China
- Guangdong Institute of Artificial Intelligence and Advanced Computing, Guangzhou, China
| | - Shan Zhao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu Qian
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Sheng-Jin Xu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu Mu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Jie Hao
- University of Chinese Academy of Sciences, Beijing, China.
- Institute of Automation, Chinese Academy of Sciences, Beijing, China.
- Guangdong Institute of Artificial Intelligence and Advanced Computing, Guangzhou, China.
| | - Jiu-Lin Du
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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4
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Zhang K, Shi X, Jiang H, Zeng K, Zhou Z, Zhai P, Zhang L, Peng H. Design and fabrication of wearable electronic textiles using twisted fiber-based threads. Nat Protoc 2024; 19:1557-1589. [PMID: 38429518 DOI: 10.1038/s41596-024-00956-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/29/2023] [Indexed: 03/03/2024]
Abstract
Mono-dimensional fiber-based electronics can effectively address the growing demand for improved wearable electronic devices because of their exceptional flexibility and stretchability. For practical applications, functional fiber electronic devices need to be integrated into more powerful and versatile systems to execute complex tasks that cannot be completed by single-fiber devices. Existing techniques, such as printing and sintering, reduce the flexibility and cause low connection strength of fiber-based electronic devices because of the high curvature of the fiber. Here, we outline a twisting fabrication process for fiber electrodes, which can be woven into functional threads and integrated within textiles. The design of the twisted thread structure for fiber devices ensures stable interfacing and good flexibility, while the textile structure features easily accessible, interlaced points for efficient circuit connections. Electronic textiles can be customized to act as displays, health monitors and power sources. We detail three main fabrication sections, including the fabrication of the fiber electrodes, their twisting into electronic threads and their assembly into functional textile-based devices. The procedures require ~10 d and are easily reproducible by researchers with expertise in fabricating energy and electronic devices.
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Affiliation(s)
- Kailin Zhang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Institute of Fiber Materials and Devices, and Laboratory of Advanced Materials, Fudan University, Shanghai, China
| | - Xiang Shi
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Institute of Fiber Materials and Devices, and Laboratory of Advanced Materials, Fudan University, Shanghai, China
| | - Haibo Jiang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Institute of Fiber Materials and Devices, and Laboratory of Advanced Materials, Fudan University, Shanghai, China
| | - Kaiwen Zeng
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Institute of Fiber Materials and Devices, and Laboratory of Advanced Materials, Fudan University, Shanghai, China
| | - Zihao Zhou
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Institute of Fiber Materials and Devices, and Laboratory of Advanced Materials, Fudan University, Shanghai, China
| | - Peng Zhai
- The Institute of AI and Robotics, Fudan University, Shanghai, China
| | - Lihua Zhang
- The Institute of AI and Robotics, Fudan University, Shanghai, China
- Ji Hua Laboratory, Foshan, Guangdong, China
| | - Huisheng Peng
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Institute of Fiber Materials and Devices, and Laboratory of Advanced Materials, Fudan University, Shanghai, China.
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5
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Dmitrijeva M, Tackmann J, Matias Rodrigues JF, Huerta-Cepas J, Coelho LP, von Mering C. A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer. Nat Ecol Evol 2024; 8:986-998. [PMID: 38443606 DOI: 10.1038/s41559-024-02357-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 02/05/2024] [Indexed: 03/07/2024]
Abstract
Horizontal gene transfer, the exchange of genetic material through means other than reproduction, is a fundamental force in prokaryotic genome evolution. Genomic persistence of horizontally transferred genes has been shown to be influenced by both ecological and evolutionary factors. However, there is limited availability of ecological information about species other than the habitats from which they were isolated, which has prevented a deeper exploration of ecological contributions to horizontal gene transfer. Here we focus on transfers detected through comparison of individual gene trees to the species tree, assessing the distribution of gene-exchanging prokaryotes across over a million environmental sequencing samples. By analysing detected horizontal gene transfer events, we show distinct functional profiles for recent versus old events. Although most genes transferred are part of the accessory genome, genes transferred earlier in evolution tend to be more ubiquitous within present-day species. We find that co-occurring, interacting and high-abundance species tend to exchange more genes. Finally, we show that host-associated specialist species are most likely to exchange genes with other host-associated specialist species, whereas species found across different habitats have similar gene exchange rates irrespective of their preferred habitat. Our study covers an unprecedented scale of integrated horizontal gene transfer and environmental information, highlighting broad eco-evolutionary trends.
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Affiliation(s)
- Marija Dmitrijeva
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zürich, Zurich, Switzerland
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zurich, Switzerland
| | - Janko Tackmann
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zürich, Zurich, Switzerland
| | | | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo-UPM, Madrid, Spain
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia.
| | - Christian von Mering
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zürich, Zurich, Switzerland.
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6
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Wang Y, Xu Y, Zhou C, Cheng Y, Qiao N, Shang Q, Xia L, Song J, Gao C, Qiao Y, Zhang X, Li M, Ma C, Fan Y, Peng X, Wu S, Lv N, Li B, Sun Y, Zhang B, Li T, Li H, Zhang J, Su Y, Li Q, Yuan J, Liu L, Moreno-De-Luca A, MacLennan AH, Gecz J, Zhu D, Wang X, Zhu C, Xing Q. Exome sequencing reveals genetic heterogeneity and clinically actionable findings in children with cerebral palsy. Nat Med 2024; 30:1395-1405. [PMID: 38693247 DOI: 10.1038/s41591-024-02912-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 03/06/2024] [Indexed: 05/03/2024]
Abstract
Cerebral palsy (CP) is the most common motor disability in children. To ascertain the role of major genetic variants in the etiology of CP, we conducted exome sequencing on a large-scale cohort with clinical manifestations of CP. The study cohort comprised 505 girls and 1,073 boys. Utilizing the current gold standard in genetic diagnostics, 387 of these 1,578 children (24.5%) received genetic diagnoses. We identified 412 pathogenic and likely pathogenic (P/LP) variants across 219 genes associated with neurodevelopmental disorders, and 59 P/LP copy number variants. The genetic diagnostic rate of children with CP labeled at birth with perinatal asphyxia was higher than the rate in children without asphyxia (P = 0.0033). Also, 33 children with CP manifestations (8.5%, 33 of 387) had findings that were clinically actionable. These results highlight the need for early genetic testing in children with CP, especially those with risk factors like perinatal asphyxia, to enable evidence-based medical decision-making.
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Affiliation(s)
- Yangong Wang
- Children's Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai, China
| | - Yiran Xu
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Chongchen Zhou
- Rehabilitation Department, Henan Key Laboratory of Child Genetics and Metabolism, Children's Hospital of Zhengzhou University, Zhengzhou, China
| | - Ye Cheng
- Children's Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai, China
- Shanghai Center for Women and Children's Health, Shanghai, China
| | - Niu Qiao
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine (Shanghai), and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qing Shang
- Rehabilitation Department, Henan Key Laboratory of Child Genetics and Metabolism, Children's Hospital of Zhengzhou University, Zhengzhou, China
| | - Lei Xia
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Juan Song
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Chao Gao
- Rehabilitation Department, Henan Key Laboratory of Child Genetics and Metabolism, Children's Hospital of Zhengzhou University, Zhengzhou, China
| | - Yimeng Qiao
- Children's Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai, China
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Xiaoli Zhang
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Ming Li
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Caiyun Ma
- Rehabilitation Department, Henan Key Laboratory of Child Genetics and Metabolism, Children's Hospital of Zhengzhou University, Zhengzhou, China
| | - Yangyi Fan
- Children's Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai, China
| | - Xirui Peng
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Silin Wu
- Department of Neurosurgery, The Affiliated Zhongshan Hospital of Fudan University, Shanghai, China
| | - Nan Lv
- Rehabilitation Department, Henan Key Laboratory of Child Genetics and Metabolism, Children's Hospital of Zhengzhou University, Zhengzhou, China
| | - Bingbing Li
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Yanyan Sun
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Bohao Zhang
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Tongchuan Li
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Hongwei Li
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Jin Zhang
- Children's Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai, China
- Shanghai Center for Women and Children's Health, Shanghai, China
| | - Yu Su
- Children's Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai, China
| | - Qiaoli Li
- Children's Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai, China
| | - Junying Yuan
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Lei Liu
- Children's Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai, China
| | - Andres Moreno-De-Luca
- Department of Radiology, Neuroradiology Section, Kingston Health Sciences Centre, Queen's University Faculty of Health Sciences, Kingston, Ontario, Canada
| | - Alastair H MacLennan
- Robinson Research Institute and Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Jozef Gecz
- Robinson Research Institute and Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Dengna Zhu
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Xiaoyang Wang
- Centre for Perinatal Medicine and Health, Institute of Clinical Science, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Changlian Zhu
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China.
| | - Qinghe Xing
- Children's Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai, China.
- Shanghai Center for Women and Children's Health, Shanghai, China.
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7
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Wu J, Li T, Guo M, Ji J, Meng X, Fu T, Nie T, Wei T, Zhou Y, Dong W, Zhang M, Shi Y, Cheng X, Yin H. Treating a type 2 diabetic patient with impaired pancreatic islet function by personalized endoderm stem cell-derived islet tissue. Cell Discov 2024; 10:45. [PMID: 38684699 PMCID: PMC11058776 DOI: 10.1038/s41421-024-00662-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 02/19/2024] [Indexed: 05/02/2024] Open
Affiliation(s)
- Jiaying Wu
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Tuo Li
- Department of Endocrinology, Shanghai Changzheng Hospital (Second Affiliated Hospital of Naval Medical University), Shanghai, China
| | - Meng Guo
- National Key Laboratory of Medical Immunology & Institute of Immunology, Naval Medical University, Shanghai, China
| | - Junsong Ji
- Organ Transplant Center, Shanghai Changzheng Hospital, Shanghai, China
| | - Xiaoxi Meng
- Department of Interventional Radiology, Shanghai Changzheng Hospital, Shanghai, China
| | - Tianlong Fu
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Tengfei Nie
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Tongkun Wei
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Ying Zhou
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Weihua Dong
- Department of Interventional Radiology, Shanghai Changzheng Hospital, Shanghai, China.
| | - Ming Zhang
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Yongquan Shi
- Department of Endocrinology, Shanghai Changzheng Hospital (Second Affiliated Hospital of Naval Medical University), Shanghai, China.
| | - Xin Cheng
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.
| | - Hao Yin
- Organ Transplant Center, Shanghai Changzheng Hospital, Shanghai, China.
- Islet Transplantation Training Base of Shanghai Endocrinology Clinical Quality Control Center, Shanghai, China.
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8
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Fu YH, Hu YF, Lin T, Zhuang GW, Wang YL, Chen WX, Li ZT, Hou JL. Constructing artificial gap junctions to mediate intercellular signal and mass transport. Nat Chem 2024:10.1038/s41557-024-01519-8. [PMID: 38658798 DOI: 10.1038/s41557-024-01519-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 03/25/2024] [Indexed: 04/26/2024]
Abstract
Natural gap junctions are a type of channel protein responsible for intercellular signalling and mass communication. However, the scope of applications for these proteins is limited as they cannot be prepared at a large scale and are unable to spontaneously insert into cell membranes in vitro. The construction of artificial gap junctions may provide an alternative strategy for preparing analogues of the natural proteins and bottom-up building blocks necessary for the synthesis of artificial cells. Here we show the construction of artificial gap junction channels from unimolecular tubular molecules consisting of alternately arranged positively and negatively charged pillar[5]arene motifs. These molecules feature a hydrophobic-hydrophilic-hydrophobic triblock structure that allows them to efficiently insert into two adjacent plasma membranes and stretch across the gap between the two membranes to form gap junctions. Similar to natural gap junction channels, the synthetic channels could mediate intercellular signal coupling and reactive oxygen species transmission, leading to cellular activity.
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Affiliation(s)
- Yong-Hong Fu
- Department of Chemistry, Fudan University, Shanghai, China
| | - Yi-Fei Hu
- Department of Chemistry, Fudan University, Shanghai, China
| | - Tao Lin
- Department of Chemistry, Fudan University, Shanghai, China
| | - Guo-Wei Zhuang
- Department of Chemistry, Fudan University, Shanghai, China
| | - Ying-Lan Wang
- Department of Chemistry, Fudan University, Shanghai, China
| | - Wen-Xue Chen
- Department of Chemistry, Fudan University, Shanghai, China
| | - Zhan-Ting Li
- Department of Chemistry, Fudan University, Shanghai, China
| | - Jun-Li Hou
- Department of Chemistry, Fudan University, Shanghai, China.
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9
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Wang C, Li J, Liu W, Zhao L, Yan H, Yan Y, Ren J, Peng L, Zhang J, Liu Y, Weng X, Zhu Y, Jing D, Mi JQ, Wang J. Refined risk stratification helps guiding transplantation choice in adult BCR::ABL1-positive acute lymphoblastic leukemia. Blood Cancer J 2024; 14:71. [PMID: 38658532 PMCID: PMC11043066 DOI: 10.1038/s41408-024-01055-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Affiliation(s)
- Cheng Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianfeng Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weiyang Liu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lingling Zhao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Han Yan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuchen Yan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiayi Ren
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lijun Peng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiaojiao Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuanfang Liu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiangqin Weng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yongmei Zhu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Duohui Jing
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jian-Qing Mi
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jin Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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10
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Guo SK, Liu CX, Xu YF, Wang X, Nan F, Huang Y, Li S, Nan S, Li L, Kon E, Li C, Wei MY, Su R, Wei J, Peng S, Ad-El N, Liu J, Peer D, Chen T, Yang L, Chen LL. Therapeutic application of circular RNA aptamers in a mouse model of psoriasis. Nat Biotechnol 2024:10.1038/s41587-024-02204-4. [PMID: 38653797 DOI: 10.1038/s41587-024-02204-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/12/2024] [Indexed: 04/25/2024]
Abstract
Efforts to advance RNA aptamers as a new therapeutic modality have been limited by their susceptibility to degradation and immunogenicity. In a previous study, we demonstrated synthesized short double-stranded region-containing circular RNAs (ds-cRNAs) with minimal immunogenicity targeted to dsRNA-activated protein kinase R (PKR). Here we test the therapeutic potential of ds-cRNAs in a mouse model of imiquimod-induced psoriasis. We find that genetic supplementation of ds-cRNAs leads to inhibition of PKR, resulting in alleviation of downstream interferon-α and dsRNA signals and attenuation of psoriasis phenotypes. Delivery of ds-cRNAs by lipid nanoparticles to the spleen attenuates PKR activity in examined splenocytes, resulting in reduced epidermal thickness. These findings suggest that ds-cRNAs represent a promising approach to mitigate excessive PKR activation for therapeutic purposes.
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Affiliation(s)
- Si-Kun Guo
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chu-Xiao Liu
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yi-Feng Xu
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiao Wang
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fang Nan
- Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Youkui Huang
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Siqi Li
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shan Nan
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ling Li
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Edo Kon
- Laboratory of Precision Nanomedicine, Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Center for Nanoscience and Nanotechnology, Cancer Biology Research Center, Tel Aviv University, Tel Aviv, Israel
| | - Chen Li
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Meng-Yuan Wei
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Rina Su
- Department of Dermatology, Beijing Chao-yang Hospital, Capital Medical University, Beijing, China
| | - Jia Wei
- Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Shiguang Peng
- Department of Dermatology, Beijing Chao-yang Hospital, Capital Medical University, Beijing, China
| | - Nitay Ad-El
- Laboratory of Precision Nanomedicine, Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Center for Nanoscience and Nanotechnology, Cancer Biology Research Center, Tel Aviv University, Tel Aviv, Israel
| | - Jiaquan Liu
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Dan Peer
- Laboratory of Precision Nanomedicine, Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Center for Nanoscience and Nanotechnology, Cancer Biology Research Center, Tel Aviv University, Tel Aviv, Israel
| | - Ting Chen
- National Institute of Biological Sciences, Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Ling-Ling Chen
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- New Cornerstone Science Laboratory, Shenzhen, China.
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
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11
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Ye X, Huang Z, Li Y, Wang M, Meng W, Miao M, Cheng J. Human tumor suppressor PDCD4 directly interacts with ribosomes to repress translation. Cell Res 2024:10.1038/s41422-024-00962-z. [PMID: 38641729 DOI: 10.1038/s41422-024-00962-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/08/2024] [Indexed: 04/21/2024] Open
Affiliation(s)
- Xianwen Ye
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China
| | - Zixuan Huang
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China
| | - Yi Li
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China
| | - Mengjiao Wang
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China
| | - Wanyu Meng
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China
| | - Maojian Miao
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China
| | - Jingdong Cheng
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China.
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12
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Wang L, Jiang W, Zhao S, Xie D, Chen Q, Zhao Q, Wu H, Luo J, Yang L. Sorafenib inhibits ossification of the posterior longitudinal ligament by blocking LOXL2-mediated vascularization. Bone Res 2024; 12:24. [PMID: 38594260 PMCID: PMC11004159 DOI: 10.1038/s41413-024-00327-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 03/10/2024] [Accepted: 03/16/2024] [Indexed: 04/11/2024] Open
Abstract
Ossification of the Posterior Longitudinal Ligament (OPLL) is a degenerative hyperostosis disease characterized by the transformation of the soft and elastic vertebral ligament into bone, resulting in limited spinal mobility and nerve compression. Employing both bulk and single-cell RNA sequencing, we elucidate the molecular characteristics, cellular components, and their evolution during the OPLL process at a single-cell resolution, and validate these findings in clinical samples. This study also uncovers the capability of ligament stem cells to exhibit endothelial cell-like phenotypes in vitro and in vivo. Notably, our study identifies LOXL2 as a key regulator in this process. Through gain-and loss-of-function studies, we elucidate the role of LOXL2 in the endothelial-like differentiation of ligament cells. It acts via the HIF1A pathway, promoting the secretion of downstream VEGFA and PDGF-BB. This function is not related to the enzymatic activity of LOXL2. Furthermore, we identify sorafenib, a broad-spectrum tyrosine kinase inhibitor, as an effective suppressor of LOXL2-mediated vascular morphogenesis. By disrupting the coupling between vascularization and osteogenesis, sorafenib demonstrates significant inhibition of OPLL progression in both BMP-induced and enpp1 deficiency-induced animal models while having no discernible effect on normal bone mass. These findings underscore the potential of sorafenib as a therapeutic intervention for OPLL.
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Affiliation(s)
- Longqing Wang
- Spine Center, Department of Orthopaedics, Shanghai Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, PR China
| | - Wenhao Jiang
- Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Tongji University School of Medicine, Shanghai, PR China
| | - Siyuan Zhao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, PR China
| | - Dong Xie
- Department of Orthopaedics, No. 905 Hospital of PLA Navy, Shanghai, PR China
| | - Qing Chen
- Spine Center, Department of Orthopaedics, Shanghai Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, PR China
| | - Qi Zhao
- Spine Center, Department of Orthopaedics, Shanghai Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, PR China
| | - Hao Wu
- Spine Center, Department of Orthopaedics, Shanghai Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, PR China
| | - Jian Luo
- Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Tongji University School of Medicine, Shanghai, PR China.
| | - Lili Yang
- Spine Center, Department of Orthopaedics, Shanghai Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, PR China.
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13
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Tang M, Jiang S, Huang X, Ji C, Gu Y, Qi Y, Xiang Y, Yao E, Zhang N, Berman E, Yu D, Qu Y, Liu L, Berry D, Yao Y. Integration of 3D bioprinting and multi-algorithm machine learning identified glioma susceptibilities and microenvironment characteristics. Cell Discov 2024; 10:39. [PMID: 38594259 PMCID: PMC11003988 DOI: 10.1038/s41421-024-00650-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 01/18/2024] [Indexed: 04/11/2024] Open
Abstract
Glioma, with its heterogeneous microenvironments and genetic subtypes, presents substantial challenges for treatment prediction and development. We integrated 3D bioprinting and multi-algorithm machine learning as a novel approach to enhance the assessment and understanding of glioma treatment responses and microenvironment characteristics. The bioprinted patient-derived glioma tissues successfully recapitulated molecular properties and drug responses of native tumors. We then developed GlioML, a machine learning workflow incorporating nine distinct algorithms and a weighted ensemble model that generated robust gene expression-based predictors, each reflecting the diverse action mechanisms of various compounds and drugs. The ensemble model superseded the performance of all individual algorithms across diverse in vitro systems, including sphere cultures, complex 3D bioprinted multicellular models, and 3D patient-derived tissues. By integrating bioprinting, the evaluative scope of the treatment expanded to T cell-related therapy and anti-angiogenesis targeted therapy. We identified promising compounds and drugs for glioma treatment and revealed distinct immunosuppressive or angiogenic myeloid-infiltrated tumor microenvironments. These insights pave the way for enhanced therapeutic development for glioma and potentially for other cancers, highlighting the broad application potential of this integrative and translational approach.
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Affiliation(s)
- Min Tang
- Shanghai University of Traditional Chinese Medicine, Shanghai, China.
- Department of NanoEngineering, University of California San Diego, La Jolla, CA, USA.
| | - Shan Jiang
- Department of Statistics, University of California Davis, Davis, CA, USA
| | - Xiaoming Huang
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- National Center for Neurological Disorders, Shanghai, China
- Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Shanghai, China
- Immunology Laboratory, Neurosurgical Institute of Fudan University, Shanghai, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China
| | - Chunxia Ji
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- National Center for Neurological Disorders, Shanghai, China
- Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Shanghai, China
- Immunology Laboratory, Neurosurgical Institute of Fudan University, Shanghai, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China
| | - Yexin Gu
- Cyberiad Biotechnology Ltd., Shanghai, China
| | - Ying Qi
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- National Center for Neurological Disorders, Shanghai, China
- Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Shanghai, China
- Immunology Laboratory, Neurosurgical Institute of Fudan University, Shanghai, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China
| | - Yi Xiang
- Department of NanoEngineering, University of California San Diego, La Jolla, CA, USA
| | - Emmie Yao
- Department of NanoEngineering, University of California San Diego, La Jolla, CA, USA
| | - Nancy Zhang
- Department of Human Biology, University of California San Diego, La Jolla, CA, USA
| | - Emma Berman
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Di Yu
- Department of Human Biology, University of California San Diego, La Jolla, CA, USA
| | - Yunjia Qu
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Longwei Liu
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - David Berry
- Department of NanoEngineering, University of California San Diego, La Jolla, CA, USA
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, USA
| | - Yu Yao
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.
- National Center for Neurological Disorders, Shanghai, China.
- Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Shanghai, China.
- Immunology Laboratory, Neurosurgical Institute of Fudan University, Shanghai, China.
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China.
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14
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Zhang Z, Wu B, Wang Y, Cai T, Ma M, You C, Liu C, Jiang G, Hu Y, Li X, Chen XZ, Song E, Cui J, Huang G, Kiravittaya S, Mei Y. Multilevel design and construction in nanomembrane rolling for three-dimensional angle-sensitive photodetection. Nat Commun 2024; 15:3066. [PMID: 38594254 PMCID: PMC11004118 DOI: 10.1038/s41467-024-47405-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 04/01/2024] [Indexed: 04/11/2024] Open
Abstract
Releasing pre-strained two-dimensional nanomembranes to assemble on-chip three-dimensional devices is crucial for upcoming advanced electronic and optoelectronic applications. However, the release process is affected by many unclear factors, hindering the transition from laboratory to industrial applications. Here, we propose a quasistatic multilevel finite element modeling to assemble three-dimensional structures from two-dimensional nanomembranes and offer verification results by various bilayer nanomembranes. Take Si/Cr nanomembrane as an example, we confirm that the three-dimensional structural formation is governed by both the minimum energy state and the geometric constraints imposed by the edges of the sacrificial layer. Large-scale, high-yield fabrication of three-dimensional structures is achieved, and two distinct three-dimensional structures are assembled from the same precursor. Six types of three-dimensional Si/Cr photodetectors are then prepared to resolve the incident angle of light with a deep neural network model, opening up possibilities for the design and manufacturing methods of More-than-Moore-era devices.
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Affiliation(s)
- Ziyu Zhang
- Department of Materials Science & State Key Laboratory of Molecular Engineering of Polymer, Fudan University, Shanghai, 200438, People's Republic of China
| | - Binmin Wu
- Department of Materials Science & State Key Laboratory of Molecular Engineering of Polymer, Fudan University, Shanghai, 200438, People's Republic of China
| | - Yang Wang
- Department of Materials Science & State Key Laboratory of Molecular Engineering of Polymer, Fudan University, Shanghai, 200438, People's Republic of China
| | - Tianjun Cai
- Department of Materials Science & State Key Laboratory of Molecular Engineering of Polymer, Fudan University, Shanghai, 200438, People's Republic of China
| | - Mingze Ma
- Department of Materials Science & State Key Laboratory of Molecular Engineering of Polymer, Fudan University, Shanghai, 200438, People's Republic of China
| | - Chunyu You
- Department of Materials Science & State Key Laboratory of Molecular Engineering of Polymer, Fudan University, Shanghai, 200438, People's Republic of China
| | - Chang Liu
- Department of Materials Science & State Key Laboratory of Molecular Engineering of Polymer, Fudan University, Shanghai, 200438, People's Republic of China
| | - Guobang Jiang
- Department of Materials Science & State Key Laboratory of Molecular Engineering of Polymer, Fudan University, Shanghai, 200438, People's Republic of China
| | - Yuhang Hu
- Department of Materials Science & State Key Laboratory of Molecular Engineering of Polymer, Fudan University, Shanghai, 200438, People's Republic of China
| | - Xing Li
- Department of Materials Science & State Key Laboratory of Molecular Engineering of Polymer, Fudan University, Shanghai, 200438, People's Republic of China
| | - Xiang-Zhong Chen
- Shanghai Frontiers Science Research Base of Intelligent Optoelectronics and Perception, Institute of Optoelectronics, Fudan University, Shanghai, 200438, People's Republic of China
- Yiwu Research Institute of Fudan University, Yiwu, 322000, Zhejiang, People's Republic of China
- International Institute of Intelligent Nanorobots and Nanosystems, Fudan University, Shanghai, 200438, People's Republic of China
| | - Enming Song
- Shanghai Frontiers Science Research Base of Intelligent Optoelectronics and Perception, Institute of Optoelectronics, Fudan University, Shanghai, 200438, People's Republic of China
- International Institute of Intelligent Nanorobots and Nanosystems, Fudan University, Shanghai, 200438, People's Republic of China
| | - Jizhai Cui
- Department of Materials Science & State Key Laboratory of Molecular Engineering of Polymer, Fudan University, Shanghai, 200438, People's Republic of China
- International Institute of Intelligent Nanorobots and Nanosystems, Fudan University, Shanghai, 200438, People's Republic of China
| | - Gaoshan Huang
- Department of Materials Science & State Key Laboratory of Molecular Engineering of Polymer, Fudan University, Shanghai, 200438, People's Republic of China
- Yiwu Research Institute of Fudan University, Yiwu, 322000, Zhejiang, People's Republic of China
- International Institute of Intelligent Nanorobots and Nanosystems, Fudan University, Shanghai, 200438, People's Republic of China
| | - Suwit Kiravittaya
- Department of Electrical Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok, Thailand
| | - Yongfeng Mei
- Department of Materials Science & State Key Laboratory of Molecular Engineering of Polymer, Fudan University, Shanghai, 200438, People's Republic of China.
- Shanghai Frontiers Science Research Base of Intelligent Optoelectronics and Perception, Institute of Optoelectronics, Fudan University, Shanghai, 200438, People's Republic of China.
- Yiwu Research Institute of Fudan University, Yiwu, 322000, Zhejiang, People's Republic of China.
- International Institute of Intelligent Nanorobots and Nanosystems, Fudan University, Shanghai, 200438, People's Republic of China.
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15
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Zhou Y, He W, Hou W, Zhu Y. Pianno: a probabilistic framework automating semantic annotation for spatial transcriptomics. Nat Commun 2024; 15:2848. [PMID: 38565531 DOI: 10.1038/s41467-024-47152-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
Spatial transcriptomics has revolutionized the study of gene expression within tissues, while preserving spatial context. However, annotating spatial spots' biological identity remains a challenge. To tackle this, we introduce Pianno, a Bayesian framework automating structural semantics annotation based on marker genes. Comprehensive evaluations underscore Pianno's remarkable prowess in precisely annotating a wide array of spatial semantics, ranging from diverse anatomical structures to intricate tumor microenvironments, as well as in estimating cell type distributions, across data generated from various spatial transcriptomics platforms. Furthermore, Pianno, in conjunction with clustering approaches, uncovers a region- and species-specific excitatory neuron subtype in the deep layer 3 of the human neocortex, shedding light on cellular evolution in the human neocortex. Overall, Pianno equips researchers with a robust and efficient tool for annotating diverse biological structures, offering new perspectives on spatial transcriptomics data.
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Affiliation(s)
- Yuqiu Zhou
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science and Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Wei He
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science and Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Weizhen Hou
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science and Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Ying Zhu
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science and Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China.
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16
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Jiang Z, Huang H, Lu C, Zhou L, Pan S, Qiang J, Shi M, Ye Z, Lu P, Ni H, Zhang W, Wu J. Ultrafast photoinduced C-H bond formation from two small inorganic molecules. Nat Commun 2024; 15:2854. [PMID: 38565554 PMCID: PMC10987588 DOI: 10.1038/s41467-024-47137-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 03/21/2024] [Indexed: 04/04/2024] Open
Abstract
The formation of carbon-hydrogen (C-H) bonds via the reaction of small inorganic molecules is of great significance for understanding the fundamental transition from inorganic to organic matter, and thus the origin of life. Yet, the detailed mechanism of the C-H bond formation, particularly the time scale and molecular-level control of the dynamics, remain elusive. Here, we investigate the light-induced bimolecular reaction starting from a van der Waals molecular dimer composed of two small inorganic molecules, H2 and CO. Employing reaction microscopy driven by a tailored two-color light field, we identify the pathways leading to C-H photobonding thereby producing HCO+ ions, and achieve coherent control over the reaction dynamics. Using a femtosecond pump-probe scheme, we capture the ultrafast formation time, i.e., 198 ± 16 femtoseconds. The real-time visualization and coherent control of the dynamics contribute to a deeper understanding of the most fundamental bimolecular reactions responsible for C-H bond formation, thus contributing to elucidate the emergence of organic components in the universe.
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Affiliation(s)
- Zhejun Jiang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200241, China
| | - Hao Huang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200241, China
| | - Chenxu Lu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200241, China
| | - Lianrong Zhou
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200241, China
| | - Shengzhe Pan
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200241, China
| | - Junjie Qiang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200241, China
| | - Menghang Shi
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200241, China
| | - Zhengjun Ye
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200241, China
| | - Peifen Lu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200241, China
| | - Hongcheng Ni
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200241, China.
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi, 030006, China.
| | - Wenbin Zhang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200241, China.
| | - Jian Wu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200241, China.
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi, 030006, China.
- Chongqing Key Laboratory of Precision Optics, Chongqing Institute of East China Normal University, Chongqing, 401121, China.
- CAS Center for Excellence in Ultra-intense Laser Science, Shanghai, 201800, China.
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17
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Wang H, Song Y, Huang G, Ding F, Ma L, Tian N, Qiu L, Li X, Zhu R, Huang S, Yan H, Chen XH, Ding L, Zheng C, Ruan W, Zhang Y. Seeded growth of single-crystal black phosphorus nanoribbons. Nat Mater 2024; 23:470-478. [PMID: 38418924 DOI: 10.1038/s41563-024-01830-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/06/2024] [Indexed: 03/02/2024]
Abstract
Two-dimensional materials have emerged as an important research frontier for overcoming the challenges in nanoelectronics and for exploring new physics. Among them, black phosphorus, with a combination of a tunable bandgap and high mobility, is one of the most promising systems. In particular, black phosphorus nanoribbons show excellent electrostatic gate control, which can mitigate short-channel effects in nanoscale transistors. Controlled synthesis of black phosphorus nanoribbons, however, has remained an outstanding problem. Here we report large-area growth of black phosphorus nanoribbons directly on insulating substrates. We seed the chemical vapour transport growth with black phosphorus nanoparticles and obtain uniform, single-crystal nanoribbons oriented exclusively along the [100] crystal direction. With comprehensive structural calculations, we discover that self-passivation at the zigzag edges holds the key to the preferential one-dimensional growth. Field-effect transistors based on individual nanoribbons exhibit on/off ratios up to ~104, confirming the good semiconducting behaviour of the nanoribbons. These results demonstrate the potential of black phosphorus nanoribbons for nanoelectronic devices and also provide a platform for investigating the exotic physics in black phosphorus.
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Affiliation(s)
- Hongya Wang
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai, China
- Shanghai Qi Zhi Institute, Shanghai, China
- Shanghai Research Center for Quantum Sciences, Shanghai, China
- Institute for Nanoelectronic Devices and Quantum Computing, Fudan University, Shanghai, China
- Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China
| | - Yichen Song
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai, China.
- Shanghai Qi Zhi Institute, Shanghai, China.
- Shanghai Research Center for Quantum Sciences, Shanghai, China.
- Institute for Nanoelectronic Devices and Quantum Computing, Fudan University, Shanghai, China.
- Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China.
| | - Guangyi Huang
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai, China
| | - Feng Ding
- Institute of Technology for Carbon Neutrality, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Liyang Ma
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai, China
- Shanghai Research Center for Quantum Sciences, Shanghai, China
- Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China
| | - Ning Tian
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai, China
- Shanghai Qi Zhi Institute, Shanghai, China
- Shanghai Research Center for Quantum Sciences, Shanghai, China
- Institute for Nanoelectronic Devices and Quantum Computing, Fudan University, Shanghai, China
- Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China
| | - Lu Qiu
- Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
- Department of Mechanical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Xian Li
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai, China
| | - Ruimin Zhu
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai, China
- Shanghai Qi Zhi Institute, Shanghai, China
- Shanghai Research Center for Quantum Sciences, Shanghai, China
- Institute for Nanoelectronic Devices and Quantum Computing, Fudan University, Shanghai, China
- Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China
| | - Shenyang Huang
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai, China
| | - Hugen Yan
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai, China
| | - Xian Hui Chen
- Key Laboratory of Strongly Coupled Quantum Matter Physics, Chinese Academy of Sciences, and Department of Physics, University of Science and Technology of China, Hefei, China.
| | - Liping Ding
- Institute of Technology for Carbon Neutrality, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- School of Electronic Information and Artificial Intelligence, Shaanxi University of Science & Technology, Xi'an, China.
| | - Changlin Zheng
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai, China.
| | - Wei Ruan
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai, China
- Shanghai Research Center for Quantum Sciences, Shanghai, China
- Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China
| | - Yuanbo Zhang
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai, China.
- Shanghai Qi Zhi Institute, Shanghai, China.
- Shanghai Research Center for Quantum Sciences, Shanghai, China.
- Institute for Nanoelectronic Devices and Quantum Computing, Fudan University, Shanghai, China.
- Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China.
- New Cornerstone Science Laboratory, Fudan University, Shanghai, China.
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18
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Semiconducting black phosphorus nanoribbons grown on insulating substrates. Nat Mater 2024; 23:458-9. [PMID: 38499744 DOI: 10.1038/s41563-024-01844-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
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19
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Liu W, Wang Z, You R, Xie C, Wei H, Xiong Y, Yang J, Zhu S. PLMSearch: Protein language model powers accurate and fast sequence search for remote homology. Nat Commun 2024; 15:2775. [PMID: 38555371 PMCID: PMC10981738 DOI: 10.1038/s41467-024-46808-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 03/08/2024] [Indexed: 04/02/2024] Open
Abstract
Homologous protein search is one of the most commonly used methods for protein annotation and analysis. Compared to structure search, detecting distant evolutionary relationships from sequences alone remains challenging. Here we propose PLMSearch (Protein Language Model), a homologous protein search method with only sequences as input. PLMSearch uses deep representations from a pre-trained protein language model and trains the similarity prediction model with a large number of real structure similarity. This enables PLMSearch to capture the remote homology information concealed behind the sequences. Extensive experimental results show that PLMSearch can search millions of query-target protein pairs in seconds like MMseqs2 while increasing the sensitivity by more than threefold, and is comparable to state-of-the-art structure search methods. In particular, unlike traditional sequence search methods, PLMSearch can recall most remote homology pairs with dissimilar sequences but similar structures. PLMSearch is freely available at https://dmiip.sjtu.edu.cn/PLMSearch .
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Affiliation(s)
- Wei Liu
- Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University, 200433, Shanghai, China
| | - Ziye Wang
- Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University, 200433, Shanghai, China
| | - Ronghui You
- Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University, 200433, Shanghai, China
| | - Chenghan Xie
- School of Mathematical Sciences, Fudan University, 200433, Shanghai, China
| | - Hong Wei
- School of Mathematical Sciences, Nankai University, 300071, Tianjin, China
| | - Yi Xiong
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Jianyi Yang
- Ministry of Education Frontiers Science Center for Nonlinear Expectations, Research Center for Mathematics and Interdisciplinary Science, Shandong University, 266237, Qingdao, China.
| | - Shanfeng Zhu
- Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University, 200433, Shanghai, China.
- Shanghai Qi Zhi Institute, Shanghai, China.
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China.
- Shanghai Key Lab of Intelligent Information Processing and Shanghai Institute of Artificial Intelligence Algorithm, Fudan University, Shanghai, China.
- Zhangjiang Fudan International Innovation Center, Shanghai, China.
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20
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Meng X, Du L, Xu S, Zhou L, Chen B, Li Y, Chen C, Ye H, Zhang J, Tian G, Bai X, Dong T, Lin W, Sun M, Zhou K, Liu Y, Zhang W, Duan S. Periodontitis exacerbates pulmonary hypertension by promoting IFNγ + T cell infiltration in mice. Int J Oral Sci 2024; 16:27. [PMID: 38548721 PMCID: PMC10978940 DOI: 10.1038/s41368-024-00291-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/23/2024] [Accepted: 02/25/2024] [Indexed: 04/01/2024] Open
Abstract
Uncovering the risk factors of pulmonary hypertension and its mechanisms is crucial for the prevention and treatment of the disease. In the current study, we showed that experimental periodontitis, which was established by ligation of molars followed by orally smearing subgingival plaques from patients with periodontitis, exacerbated hypoxia-induced pulmonary hypertension in mice. Mechanistically, periodontitis dysregulated the pulmonary microbiota by promoting ectopic colonization and enrichment of oral bacteria in the lungs, contributing to pulmonary infiltration of interferon gamma positive (IFNγ+) T cells and aggravating the progression of pulmonary hypertension. In addition, we identified Prevotella zoogleoformans as the critical periodontitis-associated bacterium driving the exacerbation of pulmonary hypertension by periodontitis, and the exacerbation was potently ameliorated by both cervical lymph node excision and IFNγ neutralizing antibodies. Our study suggests a proof of concept that the combined prevention and treatment of periodontitis and pulmonary hypertension are necessary.
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Affiliation(s)
- Xiaoqian Meng
- Department of Endodontics, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Linjuan Du
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Shuo Xu
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Lujun Zhou
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Boyan Chen
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Yulin Li
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Chumao Chen
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huilin Ye
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Jun Zhang
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Guocai Tian
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Xuebing Bai
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Ting Dong
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
- Department of Orthodontics, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenzhen Lin
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Mengjun Sun
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
- Department of Periodontology, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kecong Zhou
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
- Department of Periodontology, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Liu
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Wuchang Zhang
- Department of Endodontics, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China.
| | - Shengzhong Duan
- Department of Endodontics, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China.
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Hangzhou, China.
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21
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Yang T, Xiang CG, Wang XH, Li QQ, Lei SY, Zhang KR, Ren J, Lu HM, Feng CL, Tang W. RIPK1 inhibitor ameliorates pulmonary injury by modulating the function of neutrophils and vascular endothelial cells. Cell Death Discov 2024; 10:152. [PMID: 38521771 PMCID: PMC10960796 DOI: 10.1038/s41420-024-01921-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 03/25/2024] Open
Abstract
Acute lung injury (ALI) is an acute and progressive hypoxic respiratory failure that could progress to acute respiratory distress syndrome (ARDS) with a high mortality rate, thus immediate medical attention and supportive care are necessary. The pathophysiology of ALI is characterized by the disruption of the alveolar-capillary barrier and activation of neutrophils, leading to lung tissue damage. The receptor-interacting protein kinase 1 (RIPK1) has emerged as a promising target for the treatment of multiple inflammatory diseases, but the role of RIPK1 in the ALI remains poorly understood. In this study, we aimed to figure out the pathological role of RIPK1 in ALI, especially in the pulmonary immune microenvironment involving neutrophils and endothelial cells. In vivo experiments showed that RIPK1 inhibitor protected against lipopolysaccharide (LPS)-induced lung injury in mouse models, with reduced neutrophils and monocytes infiltration in the lungs. Further studies demonstrated that, besides the inhibitory action on necroptosis, RIPK1 inhibitor directly suppressed reactive oxygen species (ROS) generation and inflammatory cytokines secretion from neutrophils. Furthermore, RIPK1 inhibition maintains the barrier function in TNF-α-primed vascular endothelial cells and prevents their activation induced by the supernatant from LPS-stimulated neutrophils. Mechanistically, the aforementioned effects of RIPK1 inhibitor are associated with the NF-κB signaling pathway, which is partially independent of necroptosis inhibition. These results provide new evidence that RIPK1 inhibitor directly regulates the function of neutrophils and endothelial cells, as well as interferes with the interactions between these two cell types, therefore contributing to a better understanding of RIPK1 in ALI and providing a potential avenue for future therapeutic interventions.
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Affiliation(s)
- Tao Yang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cai-Gui Xiang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Han Wang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing-Qing Li
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Shu-Yue Lei
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kai-Rong Zhang
- School of Pharmaceutical Science, Nanchang University, Nanchang, 330006, China
| | - Jing Ren
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210000, China
| | - Hui-Min Lu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chun-Lan Feng
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Wei Tang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, 100049, China.
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22
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Xing M, Hu G, Wang X, Wang Y, He F, Dai W, Wang X, Niu Y, Liu J, Liu H, Zhang X, Xu J, Cai Q, Zhou D. An intranasal combination vaccine induces systemic and mucosal immunity against COVID-19 and influenza. NPJ Vaccines 2024; 9:64. [PMID: 38509167 PMCID: PMC10954707 DOI: 10.1038/s41541-024-00857-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/26/2024] [Indexed: 03/22/2024] Open
Abstract
Despite prolonged surveillance and interventions, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses continue to pose a severe global health burden. Thus, we developed a chimpanzee adenovirus-based combination vaccine, AdC68-HATRBD, with dual specificity against SARS-CoV-2 and influenza virus. When used as a standalone vaccine, intranasal immunization with AdC68-HATRBD induced comprehensive and potent immune responses consisting of immunoglobin (Ig) G, mucosal IgA, neutralizing antibodies, and memory T cells, which protected the mice from BA.5.2 and pandemic H1N1 infections. When used as a heterologous booster, AdC68-HATRBD markedly improved the protective immune response of the licensed SARS-CoV-2 or influenza vaccine. Therefore, whether administered intranasally as a standalone or booster vaccine, this combination vaccine is a valuable strategy to enhance the overall vaccine efficacy by inducing robust systemic and mucosal immune responses, thereby conferring dual lines of immunological defenses for these two viruses.
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Affiliation(s)
- Man Xing
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Gaowei Hu
- MOE&NHC&CAMS Key Laboratory of Medical Molecular, Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xiang Wang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yihan Wang
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Furong He
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Weiqian Dai
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Xinyu Wang
- MOE&NHC&CAMS Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infections Disease and Biosecurity, Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yixin Niu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Jiaojiao Liu
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Hui Liu
- Chengdu Kanghua Biological Products Co., Ltd, Chengdu, China
| | - Xiaoyan Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Jianqing Xu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
| | - Qiliang Cai
- MOE&NHC&CAMS Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infections Disease and Biosecurity, Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Dongming Zhou
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
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Li X, Zhu Q, Zhao C, Duan X, Zhao B, Zhang X, Ma H, Sun J, Lin W. Higher-order Granger reservoir computing: simultaneously achieving scalable complex structures inference and accurate dynamics prediction. Nat Commun 2024; 15:2506. [PMID: 38509083 PMCID: PMC10954644 DOI: 10.1038/s41467-024-46852-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 03/12/2024] [Indexed: 03/22/2024] Open
Abstract
Recently, machine learning methods, including reservoir computing (RC), have been tremendously successful in predicting complex dynamics in many fields. However, a present challenge lies in pushing for the limit of prediction accuracy while maintaining the low complexity of the model. Here, we design a data-driven, model-free framework named higher-order Granger reservoir computing (HoGRC), which owns two major missions: The first is to infer the higher-order structures incorporating the idea of Granger causality with the RC, and, simultaneously, the second is to realize multi-step prediction by feeding the time series and the inferred higher-order information into HoGRC. We demonstrate the efficacy and robustness of the HoGRC using several representative systems, including the classical chaotic systems, the network dynamical systems, and the UK power grid system. In the era of machine learning and complex systems, we anticipate a broad application of the HoGRC framework in structure inference and dynamics prediction.
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Affiliation(s)
- Xin Li
- Center for Applied Mathematics (NUDT), Changsha, 410073, Hunan, China
- Research Institute of Intelligent Complex Systems and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China
| | - Qunxi Zhu
- Research Institute of Intelligent Complex Systems and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China.
- School of Mathematical Sciences, SCMS, SCAM, and CCSB, Fudan University, Shanghai, 200433, China.
| | - Chengli Zhao
- Center for Applied Mathematics (NUDT), Changsha, 410073, Hunan, China.
| | - Xiaojun Duan
- Center for Applied Mathematics (NUDT), Changsha, 410073, Hunan, China
| | - Bolin Zhao
- Research Institute of Intelligent Complex Systems and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China
- School of Mathematical Sciences, SCMS, SCAM, and CCSB, Fudan University, Shanghai, 200433, China
| | - Xue Zhang
- Center for Applied Mathematics (NUDT), Changsha, 410073, Hunan, China
| | - Huanfei Ma
- School of Mathematical Sciences, Soochow University, Suzhou, 215006, China
| | - Jie Sun
- Research Institute of Intelligent Complex Systems and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China
- HUAWEI Technologies Co., Ltd., Hong Kong, China
| | - Wei Lin
- Research Institute of Intelligent Complex Systems and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China.
- School of Mathematical Sciences, SCMS, SCAM, and CCSB, Fudan University, Shanghai, 200433, China.
- Shanghai Artificial Intelligence Laboratory, Shanghai, 200232, China.
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24
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Wei L, Hai X, Xu T, Wang Z, Jiang W, Jiang S, Wang Q, Zhang YB, Zhao Y. Encoding ordered structural complexity to covalent organic frameworks. Nat Commun 2024; 15:2411. [PMID: 38499604 PMCID: PMC10948875 DOI: 10.1038/s41467-024-46849-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 03/11/2024] [Indexed: 03/20/2024] Open
Abstract
Installing different chemical entities onto crystalline frameworks with well-defined spatial distributions represents a viable approach to achieve ordered and complex synthetic materials. Herein, a covalent organic framework (COF-305) is constructed from tetrakis(4-aminophenyl)methane and 2,3-dimethoxyterephthalaldehyde, which has the largest unit cell and asymmetric unit among known COFs. The ordered complexity of COF-305 is embodied by nine different stereoisomers of its constituents showing specific sequences on topologically equivalent sites, which can be attributed to its building blocks deviating from their intrinsically preferred simple packing geometries in their molecular crystals to adapt to the framework formation. The insight provided by COF-305 supplements the principle of covalent reticular design from the perspective of non-covalent interactions and opens opportunities for pursuing complex chemical sequences in molecular frameworks.
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Affiliation(s)
- Lei Wei
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, P. R. China
| | - Xinyue Hai
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, P. R. China
| | - Tongtong Xu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, P. R. China
| | - Zidi Wang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, P. R. China
| | - Wentao Jiang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, P. R. China
| | - Shan Jiang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, P. R. China
| | - Qisheng Wang
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Yue-Biao Zhang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, P. R. China.
- Shanghai Key Laboratory of High-Resolution Electron Microscopy, ShanghaiTech University, Shanghai, 201210, China.
| | - Yingbo Zhao
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, P. R. China.
- Shanghai Key Laboratory of High-Resolution Electron Microscopy, ShanghaiTech University, Shanghai, 201210, China.
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25
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Wu Y, Li F, Wu Y, Wang H, Gu L, Zhang J, Qi Y, Meng L, Kong N, Chai Y, Hu Q, Xing Z, Ren W, Li F, Zhu X. Lanthanide luminescence nanothermometer with working wavelength beyond 1500 nm for cerebrovascular temperature imaging in vivo. Nat Commun 2024; 15:2341. [PMID: 38491065 PMCID: PMC10943110 DOI: 10.1038/s41467-024-46727-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 03/08/2024] [Indexed: 03/18/2024] Open
Abstract
Nanothermometers enable the detection of temperature changes at the microscopic scale, which is crucial for elucidating biological mechanisms and guiding treatment strategies. However, temperature monitoring of micron-scale structures in vivo using luminescent nanothermometers remains challenging, primarily due to the severe scattering effect of biological tissue that compromises the imaging resolution. Herein, a lanthanide luminescence nanothermometer with a working wavelength beyond 1500 nm is developed to achieve high-resolution temperature imaging in vivo. The energy transfer between lanthanide ions (Er3+ and Yb3+) and H2O molecules, called the environment quenching assisted downshifting process, is utilized to establish temperature-sensitive emissions at 1550 and 980 nm. Using an optimized thin active shell doped with Yb3+ ions, the nanothermometer's thermal sensitivity and the 1550 nm emission intensity are enhanced by modulating the environment quenching assisted downshifting process. Consequently, minimally invasive temperature imaging of the cerebrovascular system in mice with an imaging resolution of nearly 200 μm is achieved using the nanothermometer. This work points to a method for high-resolution temperature imaging of micron-level structures in vivo, potentially giving insights into research in temperature sensing, disease diagnosis, and treatment development.
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Affiliation(s)
- Yukai Wu
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, P.R. China
| | - Fang Li
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, P.R. China
| | - Yanan Wu
- School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, P.R. China
| | - Hao Wang
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, P.R. China
| | - Liangtao Gu
- School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, P.R. China
| | - Jieying Zhang
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, P.R. China
| | - Yukun Qi
- School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, P.R. China
| | - Lingkai Meng
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, P.R. China
| | - Na Kong
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, P.R. China
| | - Yingjie Chai
- Department of Chemistry & State Key Laboratory of Molecular Engineering of Polymers & Collaborative Innovation Center of Chemistry for Energy Materials, Fudan University, 2005 Songhu Road, Shanghai, P.R. China
| | - Qian Hu
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, P.R. China
| | - Zhenyu Xing
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, P.R. China
| | - Wuwei Ren
- School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, P.R. China.
| | - Fuyou Li
- Department of Chemistry & State Key Laboratory of Molecular Engineering of Polymers & Collaborative Innovation Center of Chemistry for Energy Materials, Fudan University, 2005 Songhu Road, Shanghai, P.R. China.
- Institute of Translational Medicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, P.R. China.
| | - Xingjun Zhu
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, P.R. China.
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26
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Liu Y, Zhang Q, Huang A, Zhang K, Wan S, Chen H, Fu Y, Zuo W, Wang Y, Cao X, Wang L, Lemmer U, Jiang W. Fully inkjet-printed Ag 2Se flexible thermoelectric devices for sustainable power generation. Nat Commun 2024; 15:2141. [PMID: 38459024 PMCID: PMC10923913 DOI: 10.1038/s41467-024-46183-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 02/16/2024] [Indexed: 03/10/2024] Open
Abstract
Flexible thermoelectric devices show great promise as sustainable power units for the exponentially increasing self-powered wearable electronics and ultra-widely distributed wireless sensor networks. While exciting proof-of-concept demonstrations have been reported, their large-scale implementation is impeded by unsatisfactory device performance and costly device fabrication techniques. Here, we develop Ag2Se-based thermoelectric films and flexible devices via inkjet printing. Large-area patterned arrays with microscale resolution are obtained in a dimensionally controlled manner by manipulating ink formulations and tuning printing parameters. Printed Ag2Se-based films exhibit (00 l)-textured feature, and an exceptional power factor (1097 μWm-1K-2 at 377 K) is obtained by engineering the film composition and microstructure. Benefiting from high-resolution device integration, fully inkjet-printed Ag2Se-based flexible devices achieve a record-high normalized power (2 µWK-2cm-2) and superior flexibility. Diverse application scenarios are offered by inkjet-printed devices, such as continuous power generation by harvesting thermal energy from the environment or human bodies. Our strategy demonstrates the potential to revolutionize the design and manufacture of multi-scale and complex flexible thermoelectric devices while reducing costs, enabling them to be integrated into emerging electronic systems as sustainable power sources.
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Affiliation(s)
- Yan Liu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, 201620, Shanghai, China
| | - Qihao Zhang
- Light Technology Institute, Karlsruhe Institute of Technology, Engesserstrasse 13, 76131, Karlsruhe, Germany.
| | - Aibin Huang
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 200050, Shanghai, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Keyi Zhang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, 201620, Shanghai, China
| | - Shun Wan
- Center for High Pressure Science and Technology Advanced Research (HPSTAR), 201203, Shanghai, China
| | - Hongyi Chen
- College of Chemistry and Chemical Engineering, Central South University, 410083, Changsha, China
| | - Yuntian Fu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, 201620, Shanghai, China
| | - Wusheng Zuo
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, 201620, Shanghai, China
| | - Yongzhe Wang
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 200050, Shanghai, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xun Cao
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 200050, Shanghai, China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, 100049, Beijing, China.
| | - Lianjun Wang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, 201620, Shanghai, China.
- Engineering Research Center of Advanced Glasses Manufacturing Technology, Ministry of Education, Donghua University, 201620, Shanghai, China.
| | - Uli Lemmer
- Light Technology Institute, Karlsruhe Institute of Technology, Engesserstrasse 13, 76131, Karlsruhe, Germany
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Wan Jiang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, 201620, Shanghai, China.
- Institute of Functional Materials, Donghua University, 201620, Shanghai, China.
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27
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Hou S, Hu J, Yu Z, Li D, Liu C, Zhang Y. Machine learning predictor PSPire screens for phase-separating proteins lacking intrinsically disordered regions. Nat Commun 2024; 15:2147. [PMID: 38459060 PMCID: PMC10923898 DOI: 10.1038/s41467-024-46445-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 02/28/2024] [Indexed: 03/10/2024] Open
Abstract
The burgeoning comprehension of protein phase separation (PS) has ushered in a wealth of bioinformatics tools for the prediction of phase-separating proteins (PSPs). These tools often skew towards PSPs with a high content of intrinsically disordered regions (IDRs), thus frequently undervaluing potential PSPs without IDRs. Nonetheless, PS is not only steered by IDRs but also by the structured modular domains and interactions that aren't necessarily reflected in amino acid sequences. In this work, we introduce PSPire, a machine learning predictor that incorporates both residue-level and structure-level features for the precise prediction of PSPs. Compared to current PSP predictors, PSPire shows a notable improvement in identifying PSPs without IDRs, which underscores the crucial role of non-IDR, structure-based characteristics in multivalent interactions throughout the PS process. Additionally, our biological validation experiments substantiate the predictive capacity of PSPire, with 9 out of 11 chosen candidate PSPs confirmed to form condensates within cells.
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Affiliation(s)
- Shuang Hou
- State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Department of Neurosurgery, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jiaojiao Hu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zhaowei Yu
- State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Department of Neurosurgery, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China.
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Yong Zhang
- State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Department of Neurosurgery, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
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28
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Zhao D, Tu S, Xu L. Efficient retrosynthetic planning with MCTS exploration enhanced A * search. Commun Chem 2024; 7:52. [PMID: 38454002 PMCID: PMC10920677 DOI: 10.1038/s42004-024-01133-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/20/2024] [Indexed: 03/09/2024] Open
Abstract
Retrosynthetic planning, which aims to identify synthetic pathways for target molecules from starting materials, is a fundamental problem in synthetic chemistry. Computer-aided retrosynthesis has made significant progress, in which heuristic search algorithms, including Monte Carlo Tree Search (MCTS) and A* search, have played a crucial role. However, unreliable guiding heuristics often cause search failure due to insufficient exploration. Conversely, excessive exploration also prevents the search from reaching the optimal solution. In this paper, MCTS exploration enhanced A* (MEEA*) search is proposed to incorporate the exploratory behavior of MCTS into A* by providing a look-ahead search. Path consistency is adopted as a regularization to improve the generalization performance of heuristics. Extensive experimental results on 10 molecule datasets demonstrate the effectiveness of MEEA*. Especially, on the widely used United States Patent and Trademark Office (USPTO) benchmark, MEEA* achieves a 100.0% success rate. Moreover, for natural products, MEEA* successfully identifies bio-retrosynthetic pathways for 97.68% test compounds.
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Affiliation(s)
- Dengwei Zhao
- Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Shikui Tu
- Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China.
| | - Lei Xu
- Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China.
- Guangdong Institute of Intelligence Science and Technology, Zhuhai, China.
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29
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Qian R, Wu M, Yang Z, Wu Y, Guo W, Zhou Z, Wang X, Li D, Lu Y. Rectifying artificial nanochannels with multiple interconvertible permeability states. Nat Commun 2024; 15:2051. [PMID: 38448408 PMCID: PMC10918189 DOI: 10.1038/s41467-024-46312-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
Transmembrane channels play a vital role in regulating the permeation process, and have inspired recent development of biomimetic channels. Herein, we report a class of artificial biomimetic nanochannels based on DNAzyme-functionalized glass nanopipettes to realize delicate control of channel permeability, whereby the surface wettability and charge can be tuned by metal ions and DNAzyme-substrates, allowing reversible conversion between different permeability states. We demonstrate that the nanochannels can be reversibly switched between four different permeability states showing distinct permeability to various functional molecules. By embedding the artificial nanochannels into the plasma membrane of single living cells, we achieve selective transport of dye molecules across the cell membrane. Finally, we report on the advanced functions including gene silencing of miR-21 in single cancer cells and selective transport of Ca2+ into single PC-12 cells. In this work, we provide a versatile tool for the design of rectifying artificial nanochannels with on-demand functions.
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Affiliation(s)
- Ruocan Qian
- Key Laboratory for Advanced Materials, East China University of Science and Technology, Shanghai, 200237, P. R. China.
- Feringa Nobel Prize Scientist Joint Research Center, Joint International Laboratory for Precision Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China.
- Frontiers Science Center for Materiobiology & Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China.
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China.
| | - Mansha Wu
- Key Laboratory for Advanced Materials, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Feringa Nobel Prize Scientist Joint Research Center, Joint International Laboratory for Precision Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Frontiers Science Center for Materiobiology & Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Zhenglin Yang
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Yuting Wu
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Weijie Guo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Zerui Zhou
- Key Laboratory for Advanced Materials, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Feringa Nobel Prize Scientist Joint Research Center, Joint International Laboratory for Precision Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Frontiers Science Center for Materiobiology & Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Xiaoyuan Wang
- Key Laboratory for Advanced Materials, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Feringa Nobel Prize Scientist Joint Research Center, Joint International Laboratory for Precision Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Frontiers Science Center for Materiobiology & Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Dawei Li
- Key Laboratory for Advanced Materials, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Feringa Nobel Prize Scientist Joint Research Center, Joint International Laboratory for Precision Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Frontiers Science Center for Materiobiology & Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA.
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
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30
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Liu Y, Hao R, Lv J, Yuan J, Wang X, Xu C, Ma D, Duan Z, Zhang B, Dai L, Cheng Y, Lu W, Zhang X. Targeted knockdown of PGAM5 in synovial macrophages efficiently alleviates osteoarthritis. Bone Res 2024; 12:15. [PMID: 38433252 PMCID: PMC10909856 DOI: 10.1038/s41413-024-00318-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/02/2024] [Accepted: 01/19/2024] [Indexed: 03/05/2024] Open
Abstract
Osteoarthritis (OA) is a common degenerative disease worldwide and new therapeutics that target inflammation and the crosstalk between immunocytes and chondrocytes are being developed to prevent and treat OA. These attempts involve repolarizing pro-inflammatory M1 macrophages into the anti-inflammatory M2 phenotype in synovium. In this study, we found that phosphoglycerate mutase 5 (PGAM5) significantly increased in macrophages in OA synovium compared to controls based on histology of human samples and single-cell RNA sequencing results of mice models. To address the role of PGAM5 in macrophages in OA, we found conditional knockout of PGAM5 in macrophages greatly alleviated OA symptoms and promoted anabolic metabolism of chondrocytes in vitro and in vivo. Mechanistically, we found that PGAM5 enhanced M1 polarization via AKT-mTOR/p38/ERK pathways, whereas inhibited M2 polarization via STAT6-PPARγ pathway in murine bone marrow-derived macrophages. Furthermore, we found that PGAM5 directly dephosphorylated Dishevelled Segment Polarity Protein 2 (DVL2) which resulted in the inhibition of β-catenin and repolarization of M2 macrophages into M1 macrophages. Conditional knockout of both PGAM5 and β-catenin in macrophages significantly exacerbated osteoarthritis compared to PGAM5-deficient mice. Motivated by these findings, we successfully designed mannose modified fluoropolymers combined with siPGAM5 to inhibit PGAM5 specifically in synovial macrophages via intra-articular injection, which possessed desired targeting abilities of synovial macrophages and greatly attenuated murine osteoarthritis. Collectively, these findings defined a key role for PGAM5 in orchestrating macrophage polarization and provides insights into novel macrophage-targeted strategy for treating OA.
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Affiliation(s)
- Yuhang Liu
- Department of Orthopedic Surgery, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200092, China
- National Facility for Translational Medicine, Shanghai, 200240, China
| | - Ruihan Hao
- Department of Orthopedic Surgery, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200092, China
- National Facility for Translational Medicine, Shanghai, 200240, China
| | - Jia Lv
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Jie Yuan
- Department of Orthopaedic Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, 030001, China
| | - Xuelei Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Churong Xu
- School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Ding Ma
- Department of Orthopedic Surgery, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200092, China
- National Facility for Translational Medicine, Shanghai, 200240, China
| | - Zhouyi Duan
- Department of Orthopedic Surgery, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200092, China
- National Facility for Translational Medicine, Shanghai, 200240, China
| | - Bingjun Zhang
- Department of Orthopedic Surgery, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200092, China
- National Facility for Translational Medicine, Shanghai, 200240, China
| | - Liming Dai
- Department of Orthopedic Surgery, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200092, China
- National Facility for Translational Medicine, Shanghai, 200240, China
| | - Yiyun Cheng
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China.
| | - Wei Lu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Xiaoling Zhang
- Department of Orthopedic Surgery, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200092, China.
- National Facility for Translational Medicine, Shanghai, 200240, China.
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31
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Zhang TY, Chen YQ, Tan JC, Zhou JA, Chen WN, Jiang T, Zha JY, Zeng XK, Li BW, Wei LQ, Zou Y, Zhang LY, Hong YM, Wang XL, Zhu RZ, Xu WX, Xi J, Wang QQ, Pan L, Zhang J, Luan Y, Zhu RX, Wang H, Chen C, Liu NN. Global fungal-host interactome mapping identifies host targets of candidalysin. Nat Commun 2024; 15:1757. [PMID: 38413612 PMCID: PMC10899660 DOI: 10.1038/s41467-024-46141-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
Candidalysin, a cytolytic peptide toxin secreted by the human fungal pathogen Candida albicans, is critical for fungal pathogenesis. Yet, its intracellular targets have not been extensively mapped. Here, we performed a high-throughput enhanced yeast two-hybrid (HT-eY2H) screen to map the interactome of all eight Ece1 peptides with their direct human protein targets and identified a list of potential interacting proteins, some of which were shared between the peptides. CCNH, a regulatory subunit of the CDK-activating kinase (CAK) complex involved in DNA damage repair, was identified as one of the host targets of candidalysin. Mechanistic studies revealed that candidalysin triggers a significantly increased double-strand DNA breaks (DSBs), as evidenced by the formation of γ-H2AX foci and colocalization of CCNH and γ-H2AX. Importantly, candidalysin binds directly to CCNH to activate CAK to inhibit DNA damage repair pathway. Loss of CCNH alleviates DSBs formation under candidalysin treatment. Depletion of candidalysin-encoding gene fails to induce DSBs and stimulates CCNH upregulation in a murine model of oropharyngeal candidiasis. Collectively, our study reveals that a secreted fungal toxin acts to hijack the canonical DNA damage repair pathway by targeting CCNH and to promote fungal infection.
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Affiliation(s)
- Tian-Yi Zhang
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yao-Qi Chen
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jing-Cong Tan
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jin-An Zhou
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Wan-Ning Chen
- Department of Gastroenterology, The Shanghai Tenth People's Hospital, Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Tong Jiang
- The Center for Microbes, Development, and Health, Key Laboratory of Molecular Virology and Immunology, Unit of Pathogenic Fungal Infection & Host Immunity, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jin-Yin Zha
- State Key Laboratory of Systems Medicine for Cancer, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China
| | - Xiang-Kang Zeng
- The Center for Microbes, Development, and Health, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Science, Shanghai, China
| | - Bo-Wen Li
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lu-Qi Wei
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yun Zou
- The Center for Microbes, Development, and Health, Key Laboratory of Molecular Virology and Immunology, Unit of Pathogenic Fungal Infection & Host Immunity, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Lu-Yao Zhang
- The Center for Microbes, Development, and Health, Key Laboratory of Molecular Virology and Immunology, Unit of Pathogenic Fungal Infection & Host Immunity, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yue-Mei Hong
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiu-Li Wang
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Run-Ze Zhu
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Wan-Xing Xu
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jing Xi
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Qin-Qin Wang
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lei Pan
- The Center for Microbes, Development, and Health, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Science, Shanghai, China
| | - Jian Zhang
- State Key Laboratory of Systems Medicine for Cancer, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China
| | - Yang Luan
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Rui-Xin Zhu
- Department of Gastroenterology, The Shanghai Tenth People's Hospital, Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Hui Wang
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Changbin Chen
- The Center for Microbes, Development, and Health, Key Laboratory of Molecular Virology and Immunology, Unit of Pathogenic Fungal Infection & Host Immunity, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Ning-Ning Liu
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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Zhou SW, Zhou D, Gu R, Ma CS, Yu C, Qu DH. Mechanically interlocked [c2]daisy chain backbone enabling advanced shape-memory polymeric materials. Nat Commun 2024; 15:1690. [PMID: 38402228 PMCID: PMC10894290 DOI: 10.1038/s41467-024-45980-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 02/09/2024] [Indexed: 02/26/2024] Open
Abstract
The incorporation of mechanically interlocked structures into polymer backbones has been shown to confer remarkable functionalities to materials. In this work, a [c2]daisy chain unit based on dibenzo-24-crown-8 is covalently embedded into the backbone of a polymer network, resulting in a synthetic material possessing remarkable shape-memory properties under thermal control. By decoupling the molecular structure into three control groups, we demonstrate the essential role of the [c2]daisy chain crosslinks in driving the shape memory function. The mechanically interlocked topology is found to be an essential element for the increase of glass transition temperature and consequent gain of shape memory function. The supramolecular host-guest interactions within the [c2]daisy chain topology not only ensure robust mechanical strength and good network stability of the polymer, but also impart the shape memory polymer with remarkable shape recovery properties and fatigue resistance ability. The incorporation of the [c2]daisy chain unit as a building block has the potential to lay the groundwork for the development of a wide range of shape-memory polymer materials.
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Affiliation(s)
- Shang-Wu Zhou
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Danlei Zhou
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Ruirui Gu
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China.
| | - Chang-Shun Ma
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Chengyuan Yu
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Da-Hui Qu
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China.
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Pang X, Wang Y, Zhu Y, Zhang Z, Xiang D, Ge X, Wu H, Jiang Y, Liu Z, Liu X, Liu C, Hu W, Zhou P. Non-volatile rippled-assisted optoelectronic array for all-day motion detection and recognition. Nat Commun 2024; 15:1613. [PMID: 38383735 PMCID: PMC10881999 DOI: 10.1038/s41467-024-46050-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 02/13/2024] [Indexed: 02/23/2024] Open
Abstract
In-sensor processing has the potential to reduce the energy consumption and hardware complexity of motion detection and recognition. However, the state-of-the-art all-in-one array integration technologies with simultaneous broadband spectrum image capture (sensory), image memory (storage) and image processing (computation) functions are still insufficient. Here, macroscale (2 × 2 mm2) integration of a rippled-assisted optoelectronic array (18 × 18 pixels) for all-day motion detection and recognition. The rippled-assisted optoelectronic array exhibits remarkable uniformity in the memory window, optically stimulated non-volatile positive and negative photoconductance. Importantly, the array achieves an extensive optical storage dynamic range exceeding 106, and exceptionally high room-temperature mobility up to 406.7 cm2 V-1 s-1, four times higher than the International Roadmap for Device and Systems 2028 target. Additionally, the spectral range of each rippled-assisted optoelectronic processor covers visible to near-infrared (405 nm-940 nm), achieving function of motion detection and recognition.
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Affiliation(s)
- Xingchen Pang
- State Key Laboratory of ASIC and System, School of Microelectronics, Fudan University, Shanghai, 200433, China
| | - Yang Wang
- State Key Laboratory of ASIC and System, School of Microelectronics, Fudan University, Shanghai, 200433, China.
- State Key Laboratory of Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, Shanghai, 200083, China.
- Shanghai Frontiers Science Research Base of Intelligent Optoelectronics and Perception, Institute of Optoelectronics, Fudan University, Shanghai, 200433, China.
| | - Yuyan Zhu
- State Key Laboratory of ASIC and System, School of Microelectronics, Fudan University, Shanghai, 200433, China
| | - Zhenhan Zhang
- State Key Laboratory of ASIC and System, School of Microelectronics, Fudan University, Shanghai, 200433, China
| | - Du Xiang
- State Key Laboratory of Integrated Chip and System, Frontier Institute of Chip and System, Fudan University, Shanghai, 200433, China.
- Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, 200433, China.
- Shanghai Qi Zhi Institute, Shanghai, 200232, China.
| | - Xun Ge
- State Key Laboratory of Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, Shanghai, 200083, China
| | - Haoqi Wu
- State Key Laboratory of ASIC and System, School of Microelectronics, Fudan University, Shanghai, 200433, China
| | - Yongbo Jiang
- State Key Laboratory of ASIC and System, School of Microelectronics, Fudan University, Shanghai, 200433, China
| | - Zizheng Liu
- State Key Laboratory of ASIC and System, School of Microelectronics, Fudan University, Shanghai, 200433, China
| | - Xiaoxian Liu
- State Key Laboratory of ASIC and System, School of Microelectronics, Fudan University, Shanghai, 200433, China
| | - Chunsen Liu
- State Key Laboratory of ASIC and System, School of Microelectronics, Fudan University, Shanghai, 200433, China
- State Key Laboratory of Integrated Chip and System, Frontier Institute of Chip and System, Fudan University, Shanghai, 200433, China
| | - Weida Hu
- State Key Laboratory of Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, Shanghai, 200083, China.
| | - Peng Zhou
- State Key Laboratory of ASIC and System, School of Microelectronics, Fudan University, Shanghai, 200433, China.
- Shanghai Frontiers Science Research Base of Intelligent Optoelectronics and Perception, Institute of Optoelectronics, Fudan University, Shanghai, 200433, China.
- State Key Laboratory of Integrated Chip and System, Frontier Institute of Chip and System, Fudan University, Shanghai, 200433, China.
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Tang S, Wang Y, Luo R, Fang R, Liu Y, Xiang H, Ran P, Tong Y, Sun M, Tan S, Huang W, Huang J, Lv J, Xu N, Yao Z, Zhang Q, Xu Z, Yue X, Yu Z, Akesu S, Ding Y, Xu C, Lu W, Zhou Y, Hou Y, Ding C. Proteomic characterization identifies clinically relevant subgroups of soft tissue sarcoma. Nat Commun 2024; 15:1381. [PMID: 38360860 PMCID: PMC10869728 DOI: 10.1038/s41467-024-45306-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 01/18/2024] [Indexed: 02/17/2024] Open
Abstract
Soft tissue sarcoma is a broad family of mesenchymal malignancies exhibiting remarkable histological diversity. We portray the proteomic landscape of 272 soft tissue sarcomas representing 12 major subtypes. Hierarchical classification finds the similarity of proteomic features between angiosarcoma and epithelial sarcoma, and elevated expression of SHC1 in AS and ES is correlated with poor prognosis. Moreover, proteomic clustering classifies patients of soft tissue sarcoma into 3 proteomic clusters with diverse driven pathways and clinical outcomes. In the proteomic cluster featured with the high cell proliferation rate, APEX1 and NPM1 are found to promote cell proliferation and drive the progression of cancer cells. The classification based on immune signatures defines three immune subtypes with distinctive tumor microenvironments. Further analysis illustrates the potential association between immune evasion markers (PD-L1 and CD80) and tumor metastasis in soft tissue sarcoma. Overall, this analysis uncovers sarcoma-type-specific changes in proteins, providing insights about relationships of soft tissue sarcoma.
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Affiliation(s)
- Shaoshuai Tang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Yunzhi Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Rongkui Luo
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Rundong Fang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Yufeng Liu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hang Xiang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Peng Ran
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Yexin Tong
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Mingjun Sun
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Subei Tan
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Wen Huang
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jie Huang
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jiacheng Lv
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Ning Xu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Zhenmei Yao
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Qiao Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Ziyan Xu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Xuetong Yue
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Zixiang Yu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Sujie Akesu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuqin Ding
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Institute of Medical Imaging, Shanghai, China
| | - Chen Xu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Weiqi Lu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Yuhong Zhou
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Chen Ding
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China.
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Li J, Pan X, Yuan Y, Shen HB. TFvelo: gene regulation inspired RNA velocity estimation. Nat Commun 2024; 15:1387. [PMID: 38360714 DOI: 10.1038/s41467-024-45661-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
RNA velocity is closely related with cell fate and is an important indicator for the prediction of cell states with elegant physical explanation derived from single-cell RNA-seq data. Most existing RNA velocity models aim to extract dynamics from the phase delay between unspliced and spliced mRNA for each individual gene. However, unspliced/spliced mRNA abundance may not provide sufficient signal for dynamic modeling, leading to poor fit in phase portraits. Motivated by the idea that RNA velocity could be driven by the transcriptional regulation, we propose TFvelo, which expands RNA velocity concept to various single-cell datasets without relying on splicing information, by introducing gene regulatory information. Our experiments on synthetic data and multiple scRNA-Seq datasets show that TFvelo can accurately fit genes dynamics on phase portraits, and effectively infer cell pseudo-time and trajectory from RNA abundance data. TFvelo opens a robust and accurate avenue for modeling RNA velocity for single cell data.
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Affiliation(s)
- Jiachen Li
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, 200240, China
| | - Xiaoyong Pan
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, 200240, China
| | - Ye Yuan
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, 200240, China.
| | - Hong-Bin Shen
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, 200240, China.
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Zhou X, Zhao C, Xu H, Xu Y, Zhan L, Wang P, He J, Lu T, Gu Y, Yang Y, Xu C, Chen Y, Liu Y, Zeng Y, Tian F, Chen Q, Xie X, Liu J, Hu H, Li J, Zheng Y, Guo J, Gao Z. Pharmacological inhibition of Kir4.1 evokes rapid-onset antidepressant responses. Nat Chem Biol 2024:10.1038/s41589-024-01555-y. [PMID: 38355723 DOI: 10.1038/s41589-024-01555-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 01/15/2024] [Indexed: 02/16/2024]
Abstract
Major depressive disorder, a prevalent and severe psychiatric condition, necessitates development of new and fast-acting antidepressants. Genetic suppression of astrocytic inwardly rectifying potassium channel 4.1 (Kir4.1) in the lateral habenula ameliorates depression-like phenotypes in mice. However, Kir4.1 remains an elusive drug target for depression. Here, we discovered a series of Kir4.1 inhibitors through high-throughput screening. Lys05, the most potent one thus far, effectively suppressed native Kir4.1 channels while displaying high selectivity against established targets for rapid-onset antidepressants. Cryogenic-electron microscopy structures combined with electrophysiological characterizations revealed Lys05 directly binds in the central cavity of Kir4.1. Notably, a single dose of Lys05 reversed the Kir4.1-driven depression-like phenotype and exerted rapid-onset (as early as 1 hour) antidepressant actions in multiple canonical depression rodent models with efficacy comparable to that of (S)-ketamine. Overall, we provided a proof of concept that Kir4.1 is a promising target for rapid-onset antidepressant effects.
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Affiliation(s)
- Xiaoyu Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- College of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Cheng Zhao
- Department of Biophysics and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haiyan Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yixiang Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Li Zhan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Pei Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jingyi He
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, Henan University, Kaifeng, China
| | - Taotao Lu
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Yueling Gu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yan Yang
- Liangzhu Laboratory, Zhejiang University School of Medicine, New Cornerstone Science Laboratory, Zhejiang University, Hangzhou, China
| | - Chanjuan Xu
- Cellular Signaling Laboratory, Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yiyang Chen
- Cellular Signaling Laboratory, Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yuxuan Liu
- Cellular Signaling Laboratory, Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yue Zeng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Fuyun Tian
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
| | - Qian Chen
- Department of Biophysics and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xin Xie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jianfeng Liu
- Cellular Signaling Laboratory, Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hailan Hu
- Liangzhu Laboratory, Zhejiang University School of Medicine, New Cornerstone Science Laboratory, Zhejiang University, Hangzhou, China
| | - Jian Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Yueming Zheng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
| | - Jiangtao Guo
- Department of Biophysics and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Zhaobing Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- College of Pharmacy, University of Chinese Academy of Sciences, Beijing, China.
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China.
- School of Pharmacy, Henan University, Kaifeng, China.
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China.
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37
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Li Z, Yang X, Fu R, Wu Z, Xu S, Jiao J, Qian M, Zhang L, Wu C, Xie T, Yao J, Wu Z, Li W, Ma G, You Y, Chen Y, Zhang HK, Cheng Y, Tang X, Wu P, Lian G, Wei H, Zhao J, Xu J, Ai L, Siwko S, Wang Y, Ding J, Song G, Luo J, Liu M, Xiao J. Kisspeptin-10 binding to Gpr54 in osteoclasts prevents bone loss by activating Dusp18-mediated dephosphorylation of Src. Nat Commun 2024; 15:1300. [PMID: 38346942 PMCID: PMC10861593 DOI: 10.1038/s41467-024-44852-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/05/2024] [Indexed: 02/15/2024] Open
Abstract
Osteoclasts are over-activated as we age, which results in bone loss. Src deficiency in mice leads to severe osteopetrosis due to a functional defect in osteoclasts, indicating that Src function is essential in osteoclasts. G-protein-coupled receptors (GPCRs) are the targets for ∼35% of approved drugs but it is still unclear how GPCRs regulate Src kinase activity. Here, we reveal that GPR54 activation by its natural ligand Kisspeptin-10 (Kp-10) causes Dusp18 to dephosphorylate Src at Tyr 416. Mechanistically, Gpr54 recruits both active Src and the Dusp18 phosphatase at its proline/arginine-rich motif in its C terminus. We show that Kp-10 binding to Gpr54 leads to the up-regulation of Dusp18. Kiss1, Gpr54 and Dusp18 knockout mice all exhibit osteoclast hyperactivation and bone loss, and Kp-10 abrogated bone loss by suppressing osteoclast activity in vivo. Therefore, Kp-10/Gpr54 is a promising therapeutic target to abrogate bone resorption by Dusp18-mediated Src dephosphorylation.
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Affiliation(s)
- Zhenxi Li
- Institute of Orthopedic Biomedical and Device Innovation, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China.
- Institute of Orthopedics, Department of Orthopedic Oncology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, 200003, China.
- East China Normal University and Shanghai Changzheng Hospital Joint Research Center for Orthopedic Oncology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.
| | - Xinghai Yang
- Institute of Orthopedics, Department of Orthopedic Oncology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Ruifeng Fu
- Institute of Orthopedic Biomedical and Device Innovation, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
- Institute of Orthopedics, Department of Orthopedic Oncology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Zhipeng Wu
- Institute of Orthopedics, Department of Orthopedic Oncology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Shengzhao Xu
- East China Normal University and Shanghai Changzheng Hospital Joint Research Center for Orthopedic Oncology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Jian Jiao
- Institute of Orthopedics, Department of Orthopedic Oncology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Ming Qian
- Institute of Orthopedics, Department of Orthopedic Oncology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Long Zhang
- Institute of Orthopedic Biomedical and Device Innovation, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Chunbiao Wu
- Institute of Orthopedic Biomedical and Device Innovation, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
- Institute of Orthopedics, Department of Orthopedic Oncology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Tianying Xie
- Institute of Orthopedic Biomedical and Device Innovation, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
- Institute of Orthopedics, Department of Orthopedic Oncology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Jiqiang Yao
- Institute of Orthopedics, Department of Orthopedic Oncology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Zhixiang Wu
- Institute of Orthopedics, Department of Orthopedic Oncology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Wenjun Li
- East China Normal University and Shanghai Changzheng Hospital Joint Research Center for Orthopedic Oncology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Guoli Ma
- East China Normal University and Shanghai Changzheng Hospital Joint Research Center for Orthopedic Oncology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yu You
- East China Normal University and Shanghai Changzheng Hospital Joint Research Center for Orthopedic Oncology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yihua Chen
- East China Normal University and Shanghai Changzheng Hospital Joint Research Center for Orthopedic Oncology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Han-Kun Zhang
- East China Normal University and Shanghai Changzheng Hospital Joint Research Center for Orthopedic Oncology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yiyun Cheng
- East China Normal University and Shanghai Changzheng Hospital Joint Research Center for Orthopedic Oncology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Xiaolong Tang
- School of Biomedical Sciences, Hunan University, Changsha, 410082, China
| | - Pengfei Wu
- Department of Neurology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Gewei Lian
- Department of Neurology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Haifeng Wei
- Institute of Orthopedics, Department of Orthopedic Oncology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Jian Zhao
- Institute of Orthopedics, Department of Orthopedic Oncology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Jianrong Xu
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Lianzhong Ai
- Institute of Orthopedic Biomedical and Device Innovation, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Stefan Siwko
- Department of Translational Medical Sciences, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX, USA
| | - Yue Wang
- Shanghai Key Lab of Cell Engineering; Translational Medicine Research Center, Naval Medical University, Shanghai, 200433, China
| | - Jin Ding
- Clinical Cancer Institute, Center for Translational Medicine, Naval Medical University, Shanghai, 200433, China
| | - Gaojie Song
- East China Normal University and Shanghai Changzheng Hospital Joint Research Center for Orthopedic Oncology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Jian Luo
- Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Tongji University School of Medicine, Shanghai, China
| | - Mingyao Liu
- East China Normal University and Shanghai Changzheng Hospital Joint Research Center for Orthopedic Oncology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Jianru Xiao
- Institute of Orthopedic Biomedical and Device Innovation, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
- Institute of Orthopedics, Department of Orthopedic Oncology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
- East China Normal University and Shanghai Changzheng Hospital Joint Research Center for Orthopedic Oncology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
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Wu X, Jiang L, Qi H, Hu C, Jia X, Lin H, Wang S, Lin L, Zhang Y, Zheng R, Li M, Wang T, Zhao Z, Xu M, Xu Y, Chen Y, Zheng J, Bi Y, Lu J. Brain tissue- and cell type-specific eQTL Mendelian randomization reveals efficacy of FADS1 and FADS2 on cognitive function. Transl Psychiatry 2024; 14:77. [PMID: 38316767 PMCID: PMC10844634 DOI: 10.1038/s41398-024-02784-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 01/08/2024] [Accepted: 01/16/2024] [Indexed: 02/07/2024] Open
Abstract
Epidemiological studies suggested an association between omega-3 fatty acids and cognitive function. However, the causal role of the fatty acid desaturase (FADS) gene, which play a key role in regulating omega-3 fatty acids biosynthesis, on cognitive function is unclear. Hence, we used two-sample Mendelian randomization (MR) to estimate the gene-specific causal effect of omega-3 fatty acids (N = 114,999) on cognitive function (N = 300,486). Tissue- and cell type-specific effects of FADS1/FADS2 expression on cognitive function were estimated using brain tissue cis-expression quantitative trait loci (cis-eQTL) datasets (GTEx, N ≤ 209; MetaBrain, N ≤ 8,613) and single cell cis-eQTL data (N = 373), respectively. These causal effects were further evaluated in whole blood cis-eQTL data (N ≤ 31,684). A series of sensitivity analyses were conducted to validate MR assumptions. Leave-one-out MR showed a FADS gene-specific effect of omega-3 fatty acids on cognitive function [β = -1.3 × 10-2, 95% confidence interval (CI) (-2.2 × 10-2, -5 × 10-3), P = 2 × 10-3]. Tissue-specific MR showed an effect of increased FADS1 expression in cerebellar hemisphere and FADS2 expression in nucleus accumbens basal ganglia on maintaining cognitive function, while decreased FADS1 expression in nine brain tissues on maintaining cognitive function [colocalization probability (PP.H4) ranged from 71.7% to 100.0%]. Cell type-specific MR showed decreased FADS1/FADS2 expression in oligodendrocyte was associated with maintaining cognitive function (PP.H4 = 82.3%, respectively). Increased FADS1/FADS2 expression in whole blood showed an effect on cognitive function maintenance (PP.H4 = 86.6% and 88.4%, respectively). This study revealed putative causal effect of FADS1/FADS2 expression in brain tissues and blood on cognitive function. These findings provided evidence to prioritize FADS gene as potential target gene for maintenance of cognitive function.
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Affiliation(s)
- Xueyan Wu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Endocrine and Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Jiang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Endocrine and Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongyan Qi
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Endocrine and Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chunyan Hu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Endocrine and Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaojing Jia
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Endocrine and Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hong Lin
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Endocrine and Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuangyuan Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Endocrine and Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin Lin
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Endocrine and Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yifang Zhang
- Network and Information Center, Shanghai Jiao Tong University, Shanghai, China
| | - Ruizhi Zheng
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Endocrine and Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mian Li
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Endocrine and Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tiange Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Endocrine and Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhiyun Zhao
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Endocrine and Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min Xu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Endocrine and Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Xu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Endocrine and Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuhong Chen
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Endocrine and Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Zheng
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai National Clinical Research Center for Endocrine and Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai Digital Medicine Innovation Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.
| | - Yufang Bi
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai National Clinical Research Center for Endocrine and Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jieli Lu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai National Clinical Research Center for Endocrine and Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Chen Y, Chen J, Wang H, Yu Y, Wang W, Liu W, Yu S, Gong Y, Jia H, Li T, Sun X. Prevalence and optical coherence tomography analyses of outer retinal tubulations in Chinese population with inherited retinal diseases. Eye (Lond) 2024; 38:328-334. [PMID: 37553355 PMCID: PMC10810923 DOI: 10.1038/s41433-023-02686-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 07/14/2023] [Accepted: 07/26/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND To investigate the prevalence of outer retinal tubulation (ORT) and its correlations with optical coherence tomography (OCT) parameters in Chinese population with inherited retinal diseases (IRDs). METHODS This retrospective study enrolled consecutive patients identified with IRDs and referred for genetic testing between February 2016 and April 2021. Clinical characteristics from medical records and features of cross-sectional B-scans were reviewed and analysed. The associations of patient-specific and ocular features with the presence of ORT were evaluated using univariate and multivariate analyses. RESULTS Two hundred and three patients (401 eyes) with a mean age of 49.7 ± 16.7 years were enrolled. ORT was observed in 41 eyes (10.2%), including 26 of 28 eyes (92.9%) with Bietti crystalline corneoretinal dystrophy (BCD), 14 of 338 eyes (4.1%) with retinitis pigmentosa (RP), and 1 of 26 eyes (3.8%) in eyes with cone-rod dystrophy. Eyes with ORT showed significantly worse visual acuity than those without ORT (P = 0.002). Multivariate analysis indicated that the presence of ORT was positively correlated with choroidal atrophy and inner nuclear layer (INL) cysts (P < 0.01). ORTs were detected more frequently in eyes with BCD than RP (P = 0.024), most of which located exclusively within the extrafoveal area. Large choroidal vessels were detected underneath the corresponding ORTs in both patients with BCD and RP. CONCLUSIONS The prevalence of ORT varies among different IRDs phenotypes, with the highest prevalence in BCD. The presence of choroidal atrophy and INL cysts may be associated with an increased risk of ORT formation in patients with IRD.
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Affiliation(s)
- Yuhong Chen
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Clinical Research Center for Ophthalmic Diseases, Shanghai, China
| | - Jieqiong Chen
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Clinical Research Center for Ophthalmic Diseases, Shanghai, China
| | - Hong Wang
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Clinical Research Center for Ophthalmic Diseases, Shanghai, China
| | - Yang Yu
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenqiu Wang
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Clinical Research Center for Ophthalmic Diseases, Shanghai, China
| | - Wenjia Liu
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Clinical Research Center for Ophthalmic Diseases, Shanghai, China
| | - Suqin Yu
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Clinical Research Center for Ophthalmic Diseases, Shanghai, China
| | - Yuanyuan Gong
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Clinical Research Center for Ophthalmic Diseases, Shanghai, China
| | - Huixun Jia
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Clinical Research Center for Ophthalmic Diseases, Shanghai, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Tong Li
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- National Clinical Research Center for Ophthalmic Diseases, Shanghai, China.
| | - Xiaodong Sun
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- National Clinical Research Center for Ophthalmic Diseases, Shanghai, China.
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China.
- Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.
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40
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Huang ME, Qin Y, Shang Y, Hao Q, Zhan C, Lian C, Luo S, Liu LD, Zhang S, Zhang Y, Wo Y, Li N, Wu S, Gui T, Wang B, Luo Y, Cai Y, Liu X, Xu Z, Dai P, Li S, Zhang L, Dong J, Wang J, Zheng X, Xu Y, Sun Y, Wu W, Yeap LS, Meng FL. C-to-G editing generates double-strand breaks causing deletion, transversion and translocation. Nat Cell Biol 2024; 26:294-304. [PMID: 38263276 DOI: 10.1038/s41556-023-01342-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 12/19/2023] [Indexed: 01/25/2024]
Abstract
Base editors (BEs) introduce base substitutions without double-strand DNA cleavage. Besides precise substitutions, BEs generate low-frequency 'stochastic' byproducts through unclear mechanisms. Here, we performed in-depth outcome profiling and genetic dissection, revealing that C-to-G BEs (CGBEs) generate substantial amounts of intermediate double-strand breaks (DSBs), which are at the centre of several byproducts. Imperfect DSB end-joining leads to small deletions via end-resection, templated insertions or aberrant transversions during end fill-in. Chromosomal translocations were detected between the editing target and off-targets of Cas9/deaminase origin. Genetic screenings of DNA repair factors disclosed a central role of abasic site processing in DSB formation. Shielding of abasic sites by the suicide enzyme HMCES reduced CGBE-initiated DSBs, providing an effective way to minimize DSB-triggered events without affecting substitutions. This work demonstrates that CGBEs can initiate deleterious intermediate DSBs and therefore require careful consideration for therapeutic applications, and that HMCES-aided CGBEs hold promise as safer tools.
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Affiliation(s)
- Min Emma Huang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Yining Qin
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Yafang Shang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Qian Hao
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Endocrinology and Metabolic Diseases, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chuanzong Zhan
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Endocrinology and Metabolic Diseases, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chaoyang Lian
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Simin Luo
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liu Daisy Liu
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Senxin Zhang
- Department of Mathematics, Shanghai Normal University, Shanghai, China
| | - Yu Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yang Wo
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Institute of Thoracic Oncology, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Niu Li
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuheng Wu
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Tuantuan Gui
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Binbin Wang
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yifeng Luo
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Yanni Cai
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Xiaojing Liu
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Ziye Xu
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Pengfei Dai
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Simiao Li
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Liang Zhang
- Hefei National Research Center for Cross Disciplinary Science, Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Junchao Dong
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jian Wang
- International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoqi Zheng
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingjie Xu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yihua Sun
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Institute of Thoracic Oncology, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wei Wu
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Leng-Siew Yeap
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Department of Endocrinology and Metabolic Diseases, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Fei-Long Meng
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China.
- Shanghai Sci-Tech Inno Center for Infection & Immunity, Shanghai, China.
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Li J, Gong S, Gao S, Chen J, Chen WW, Zhao B. Asymmetric α-C(sp 3)-H allylic alkylation of primary alkylamines by synergistic Ir/ketone catalysis. Nat Commun 2024; 15:939. [PMID: 38296941 PMCID: PMC10830461 DOI: 10.1038/s41467-024-45131-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 01/12/2024] [Indexed: 02/02/2024] Open
Abstract
Primary alkyl amines are highly reactive in N-nucleophilic reactions with electrophiles. However, their α-C-H bonds are unreactive towards electrophiles due to their extremely low acidity (pKa ~57). Nonetheless, 1,8-diazafluoren-9-one (DFO) can activate primary alkyl amines by increasing the acidity of the α-amino C-H bonds by up to 1044 times. This makes the α-amino C-H bonds acidic enough to be deprotonated under mild conditions. By combining DFO with an iridium catalyst, direct asymmetric α-C-H alkylation of NH2-unprotected primary alkyl amines with allylic carbonates has been achieved. This reaction produces a wide range of chiral homoallylic amines with high enantiopurities. The approach has successfully switched the reactivity between primary alkyl amines and allylic carbonates from intrinsic allylic amination to the α-C-H alkylation, enabling the construction of pharmaceutically significant chiral homoallylic amines from readily available primary alkyl amines in a single step.
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Affiliation(s)
- Jianyu Li
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Frontiers Science Center of Biomimetic Catalysis and Shanghai Normal University, Shanghai, 200234, China
| | - Sheng Gong
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Frontiers Science Center of Biomimetic Catalysis and Shanghai Normal University, Shanghai, 200234, China
| | - Shaolun Gao
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Frontiers Science Center of Biomimetic Catalysis and Shanghai Normal University, Shanghai, 200234, China
| | - Jianfeng Chen
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Frontiers Science Center of Biomimetic Catalysis and Shanghai Normal University, Shanghai, 200234, China.
| | - Wen-Wen Chen
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Frontiers Science Center of Biomimetic Catalysis and Shanghai Normal University, Shanghai, 200234, China
| | - Baoguo Zhao
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Frontiers Science Center of Biomimetic Catalysis and Shanghai Normal University, Shanghai, 200234, China.
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Lin K, Zhao Y, Tang Y, Chen Y, Lin M, He L. Collagen I-induced VCAN/ERK signaling and PARP1/ZEB1-mediated metastasis facilitate OSBPL2 defect to promote colorectal cancer progression. Cell Death Dis 2024; 15:85. [PMID: 38267463 PMCID: PMC10808547 DOI: 10.1038/s41419-024-06468-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/26/2024]
Abstract
The global burden of colorectal cancer (CRC) has rapidly increased in recent years. Dysregulated cholesterol homeostasis facilitated by extracellular matrix (ECM) remodeling transforms the tumor microenvironment. Collagen I, a major with ECM component is highly expressed in colorectal tumors with infiltrative growth. Although oxysterol binding protein (OSBP)-related proteins accommodate tumorigenesis, OSBPL2, which is usually involved in deafness, is not associated with CRC progression. Therefore, we aimed to investigate the pathological function of OSBPL2 and identify the molecular link between ECM-Collagen I and OSBPL2 in CRC to facilitate the development of new treatments for CRC. OSBPL2 predicted a favorable prognosis in stage IV CRC and substantially repressed Collagen I-induced focal adhesion, migration, and invasion. The reduction of OSBPL2 activated ERK signaling through the VCAN/AREG/EREG axis during CRC growth, while relying on PARP1 via ZEB1 in CRC metastasis. OSBPL2 defect supported colorectal tumor growth and metastasis, which were suppressed by the ERK and PARP1 inhibitors SCH772984 and AG14361, respectively. Overall, our findings revealed that the Collagen I-induced loss of OSBPL2 aggravates CRC progression through VCAN-mediated ERK signaling and the PARP1/ZEB1 axis. This demonstrates that SCH772984 and AG14361 are reciprocally connective therapies for OSBPL2Low CRC, which could contribute to further development of targeted CRC treatment.
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Affiliation(s)
- Kang Lin
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Gastrointestinal Surgery and Translational Medicine, School of Medicine, Tongji University, Shanghai, China
| | - Yun Zhao
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Yuqi Tang
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Gastrointestinal Surgery and Translational Medicine, School of Medicine, Tongji University, Shanghai, China
| | - Ying Chen
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Gastrointestinal Surgery and Translational Medicine, School of Medicine, Tongji University, Shanghai, China
| | - Moubin Lin
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China.
- Institute of Gastrointestinal Surgery and Translational Medicine, School of Medicine, Tongji University, Shanghai, China.
- Department of General Surgery, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China.
| | - Luwei He
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China.
- Institute of Gastrointestinal Surgery and Translational Medicine, School of Medicine, Tongji University, Shanghai, China.
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43
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Jia Y, Yang Q, Fang YW, Lu Y, Xie M, Wei J, Tian J, Zhang L, Yang R. Giant tunnelling electroresistance in atomic-scale ferroelectric tunnel junctions. Nat Commun 2024; 15:693. [PMID: 38267445 PMCID: PMC10808203 DOI: 10.1038/s41467-024-44927-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 01/11/2024] [Indexed: 01/26/2024] Open
Abstract
Ferroelectric tunnel junctions are promising towards high-reliability and low-power non-volatile memories and computing devices. Yet it is challenging to maintain a high tunnelling electroresistance when the ferroelectric layer is thinned down towards atomic scale because of the ferroelectric structural instability and large depolarization field. Here we report ferroelectric tunnel junctions based on samarium-substituted layered bismuth oxide, which can maintain tunnelling electroresistance of 7 × 105 with the samarium-substituted bismuth oxide film down to one nanometer, three orders of magnitude higher than previous reports with such thickness, owing to efficient barrier modulation by the large ferroelectric polarization. These ferroelectric tunnel junctions demonstrate up to 32 resistance states without any write-verify technique, high endurance (over 5 × 109), high linearity of conductance modulation, and long retention time (10 years). Furthermore, tunnelling electroresistance over 109 is achieved in ferroelectric tunnel junctions with 4.6-nanometer samarium-substituted bismuth oxide layer, which is higher than commercial flash memories. The results show high potential towards multi-level and reliable non-volatile memories.
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Affiliation(s)
- Yueyang Jia
- University of Michigan-Shanghai Jiao Tong University Joint Institute, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qianqian Yang
- Beijing Advanced Innovation Center for Materials Genome Engineering, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, 100083, China
| | - Yue-Wen Fang
- Fisika Aplikatua Saila, Gipuzkoako Ingeniaritza Eskola, University of the Basque Country (UPV/EHU), Europa Plaza 1, 20018, Donostia/San Sebastián, Spain.
- Centro de Física de Materiales (CSIC-UPV/EHU), Manuel de Lardizabal Pasealekua 5, 20018, Donostia/San Sebastián, Spain.
| | - Yue Lu
- Beijing Key Laboratory of Microstructure and Properties of Solids, Faculty of Materials and Manufacturing, Beijing, University of Technology, Beijing, 100124, China
| | - Maosong Xie
- University of Michigan-Shanghai Jiao Tong University Joint Institute, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jianyong Wei
- University of Michigan-Shanghai Jiao Tong University Joint Institute, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jianjun Tian
- Beijing Advanced Innovation Center for Materials Genome Engineering, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, 100083, China
| | - Linxing Zhang
- Beijing Advanced Innovation Center for Materials Genome Engineering, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, 100083, China.
| | - Rui Yang
- University of Michigan-Shanghai Jiao Tong University Joint Institute, Shanghai Jiao Tong University, Shanghai, 200240, China.
- State Key Laboratory of Radio Frequency Heterogeneous Integration, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Zhu Y, Wang Q, Xie X, Ma C, Qiao Y, Zhang Y, Wu Y, Gao Y, Jiang J, Liu X, Chen J, Li C, Ge G. ZBTB7B is a permissive regulator of hepatocellular carcinoma initiation by repressing c-Jun expression and function. Cell Death Dis 2024; 15:55. [PMID: 38225233 PMCID: PMC10789742 DOI: 10.1038/s41419-024-06441-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 01/02/2024] [Accepted: 01/05/2024] [Indexed: 01/17/2024]
Abstract
Hepatocarcinogenesis is a multi-step process. However, the regulators of hepatocellular carcinoma (HCC) initiation are understudied. Adult liver-specific gene expression was globally downregulated in HCC. We hypothesize that adult liver-specific genes, especially adult liver-enriched transcription factors may exert tumor-suppressive functions in HCC. In this study, we identify ZBTB7B, an adult liver-enriched transcription factor as a permissive regulator of HCC initiation. ZBTB7B is highly expressed in hepatocytes in adult livers, compared to fetal livers. To evaluate the functions of ZBTB7B in hepatocarcinogenesis, we performed hepatocyte-specific ZBTB7B knockout in hydrodynamic oncogene transfer-induced mouse liver cancer models. Hepatocyte-specific knockout of ZBTB7B promotes activated Akt and N-Ras-induced HCC development. Moreover, ZBTB7B deficiency sensitizes hepatocytes to a single oncogene Akt-induced oncogenic transformation and HCC initiation, which is otherwise incompetent in inducing HCC. ZBTB7B deficiency accelerates HCC initiation by down-regulating adult liver-specific gene expression and priming livers to a fetal-like state. The molecular mechanism underlying ZBTB7B functions in hepatocytes was investigated by integrated transcriptomic, phosphoproteomic, and chromatin immunoprecipitation-sequencing analyses. Integrative multi-omics analyses identify c-Jun as the core signaling node in ZBTB7B-deficient liver cancer initiation. c-Jun is a direct target of ZBTB7B essential to accelerated liver cancer initiation in ZBTB7B-deficient livers. Knockdown of c-Jun expression or dominant negative c-Jun expression delays HCC development in ZBTB7B-deficient livers. In addition, ZBTB7B competes with c-Jun for chromatin binding. Ectopic ZBTB7B expression attenuates the tumor-promoting functions of c-Jun. Expression of ZBTB7B signature, composed of 140 genes co-regulated by ZBTB7B and c-Jun, is significantly downregulated in early-stage HCCs compared to adjacent normal tissues, correlates to liver-specific gene expression, and is associated with good prognosis in human HCC. Thus, ZBTB7B functions as a permissive regulator of HCC initiation by directly regulating c-Jun expression and function.
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Affiliation(s)
- Yue Zhu
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Qinqin Wang
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xinyu Xie
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Cuihong Ma
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yuemei Qiao
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yu Zhang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yanjun Wu
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yuan Gao
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jing Jiang
- Genome Tagging Project (GTP) Center, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xin Liu
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jianfeng Chen
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Chen Li
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Gaoxiang Ge
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
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Zhang B, Rolls ET, Wang X, Xie C, Cheng W, Feng J. Roles of the medial and lateral orbitofrontal cortex in major depression and its treatment. Mol Psychiatry 2024:10.1038/s41380-023-02380-w. [PMID: 38212376 DOI: 10.1038/s41380-023-02380-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 12/06/2023] [Accepted: 12/13/2023] [Indexed: 01/13/2024]
Abstract
We describe evidence for dissociable roles of the medial and lateral orbitofrontal cortex (OFC) in major depressive disorder (MDD) from structure, functional activation, functional connectivity, metabolism, and neurochemical systems. The reward-related medial orbitofrontal cortex has lower connectivity and less reward sensitivity in MDD associated with anhedonia symptoms; and the non-reward related lateral OFC has higher functional connectivity and more sensitivity to non-reward/aversive stimuli in MDD associated with negative bias symptoms. Importantly, we propose that conventional antidepressants act to normalize the hyperactive lateral (but not medial) OFC to reduce negative bias in MDD; while other treatments are needed to operate on the medial OFC to reduce anhedonia, with emerging evidence suggesting that ketamine may act in this way. The orbitofrontal cortex is the key cortical region in emotion and reward, and the current review presents much new evidence about the different ways that the medial and lateral OFC are involved in MDD.
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Affiliation(s)
- Bei Zhang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, PR China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, PR China
| | - Edmund T Rolls
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, PR China.
- Oxford Centre for Computational Neuroscience, Oxford, UK.
- Department of Computer Science, University of Warwick, Coventry, UK.
| | - Xiang Wang
- Medical Psychological Center, The Second Xiangya Hospital, Central South University, Changsha, PR China
- Medical Psychological Institute, Central South University, Changsha, PR China
- China National Clinical Research Center on Mental Disorders (Xiangya), Changsha, PR China
| | - Chao Xie
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, PR China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, PR China
| | - Wei Cheng
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, PR China.
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, PR China.
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai, PR China.
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, PR China.
| | - Jianfeng Feng
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, PR China.
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, PR China.
- Department of Computer Science, University of Warwick, Coventry, UK.
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai, PR China.
- Zhangjiang Fudan International Innovation Center, Shanghai, PR China.
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Wang L, Jiao F, Jiang H, Yang Y, Huang Z, Wang Q, Xu W, Zhu Y, Xia S, Jiang S, Lu L. Fusogenicity of SARS-CoV-2 BA.2.86 subvariant and its sensitivity to the prokaryotic recombinant EK1 peptide. Cell Discov 2024; 10:6. [PMID: 38191587 PMCID: PMC10774434 DOI: 10.1038/s41421-023-00631-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 11/28/2023] [Indexed: 01/10/2024] Open
Affiliation(s)
- Lijue Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Fudan University, Shanghai, China
| | - Fanke Jiao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Fudan University, Shanghai, China
| | - Hanxiao Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Fudan University, Shanghai, China
| | - Yitao Yang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Fudan University, Shanghai, China
| | - Ziqi Huang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Fudan University, Shanghai, China
| | - Qian Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Fudan University, Shanghai, China
| | - Wei Xu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Fudan University, Shanghai, China
| | - Yun Zhu
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Shuai Xia
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Fudan University, Shanghai, China.
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Fudan University, Shanghai, China.
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Fudan University, Shanghai, China.
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Wang H, Cheng L, Yu J, Si Y, Ding B. Biomimetic Bouligand chiral fibers array enables strong and superelastic ceramic aerogels. Nat Commun 2024; 15:336. [PMID: 38184664 PMCID: PMC10771491 DOI: 10.1038/s41467-023-44657-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 12/22/2023] [Indexed: 01/08/2024] Open
Abstract
Ceramic aerogels are often used when thermal insulation materials are desired; however, they are still plagued by poor mechanical stability under thermal shock. Here, inspired by the dactyl clubs of mantis shrimp found in nature, which form by directed assembly into hierarchical, chiral and Bouligand (twisted plywood) structure exhibiting superior mechanical properties, we present a compositional and structural engineering strategy to develop strong, superelastic and fatigue resistance ceramic aerogels with chiral fibers array resembling Bouligand architecture. Benefiting from the stress dissipation, crack torsion and mechanical reinforcement of micro-/nano-scale Bouligand array, the tensile strength of these aerogels (170.38 MPa) is between one and two orders of magnitude greater than that of state-of-the-art nanofibrous aerogels. In addition, the developed aerogels feature low density and thermal conductivity, good compressive properties with rapid recovery from 80 % strain, and thermal stability up to 1200 °C, making them ideal for thermal insulation applications.
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Affiliation(s)
- Hongxing Wang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Textiles, Donghua University, 201620, Shanghai, China
| | - Longdi Cheng
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Textiles, Donghua University, 201620, Shanghai, China
| | - Jianyong Yu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Textiles, Donghua University, 201620, Shanghai, China
- Innovation Center for Textile Science and Technology, Donghua University, 200051, Shanghai, China
| | - Yang Si
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Textiles, Donghua University, 201620, Shanghai, China.
- Innovation Center for Textile Science and Technology, Donghua University, 200051, Shanghai, China.
| | - Bin Ding
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Textiles, Donghua University, 201620, Shanghai, China.
- Innovation Center for Textile Science and Technology, Donghua University, 200051, Shanghai, China.
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Zhang Y, Guo C, Zhou Y, Zhang W, Zhu Z, Wang W, Wan Y. A biphenotypic lymphocyte subset displays both T- and B-cell functionalities. Commun Biol 2024; 7:28. [PMID: 38182721 PMCID: PMC10770049 DOI: 10.1038/s42003-023-05719-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 12/18/2023] [Indexed: 01/07/2024] Open
Abstract
T cell/B cell mixed phenotypic lymphocytes have been observed in different disease contexts, yet their presence and function in physiological conditions remain elusive. Here, we provide evidence for the existence of a lymphocyte subset endogenously expressing both T- and B-cell lineage markers in mice. The majority of these T/B phenotypic lymphocytes (CD3+CD19+) show an origin of pro/pre B cells and distribute widely in mouse bone marrow, lymph nodes, spleen, and peripheral blood. Functional assays show that these biphenotypic lymphocytes can be activated through stimulating TCR or BCR signaling pathways. Moreover, we show that these cells actively participate both the humoral and cellular immune responses elicited by vaccination. Compared to conventional T cells, these biphenotypic lymphocytes can secrete a higher level of IL-2 but a lower level of TNF-α upon antigen specific stimulation. An equivalent lymphocyte subset is found in freshly isolated human PBMCs and exhibits similar functionality, albeit at a lower frequency than in mice.
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Affiliation(s)
- Yifan Zhang
- Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Laboratory of Laboratory Medicine of Henan Province, Zhengzhou, China
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Shanghai, China
| | - Cuiyuan Guo
- Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Laboratory of Laboratory Medicine of Henan Province, Zhengzhou, China
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Shanghai, China
| | - Yigong Zhou
- Life Science Department, Faculty of Agricultural and Environmental Sciences, Macdonald Campus of McGill University, Quebec, Canada
| | - Wenhong Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhaoqin Zhu
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Shanghai, China.
| | - Wanhai Wang
- Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Laboratory of Laboratory Medicine of Henan Province, Zhengzhou, China.
| | - Yanmin Wan
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.
- Shanghai Huashen Institute of Microbes and Infections, Shanghai, China.
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Cui S, Xia T, Zhao J, Ren X, Wu T, Kameni M, Guo X, He L, Guo J, Duperray-Susini A, Levillayer F, Collard JM, Zhong J, Pan L, Tangy F, Vidalain PO, Zhou D, Jiu Y, Faure M, Wei Y. NDP52 mediates an antiviral response to hepatitis B virus infection through Rab9-dependent lysosomal degradation pathway. Nat Commun 2023; 14:8440. [PMID: 38114531 PMCID: PMC10730550 DOI: 10.1038/s41467-023-44201-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023] Open
Abstract
Autophagy receptor NDP52 triggers bacterial autophagy against infection. However, the ability of NDP52 to protect against viral infection has not been established. We show that NDP52 binds to envelope proteins of hepatitis B virus (HBV) and triggers a degradation process that promotes HBV clearance. Inactivating NDP52 in hepatocytes results in decreased targeting of viral envelopes in the lysosome and increased levels of viral replication. NDP52 inhibits HBV at both viral entry and late replication stages. In contrast to NDP52-mediated bacterial autophagy, lysosomal degradation of HBV envelopes is independent of galectin 8 and ATG5. NDP52 forms complex with Rab9 and viral envelope proteins and links HBV to Rab9-dependent lysosomal degradation pathway. These findings reveal that NDP52 acts as a sensor for HBV infection, which mediates a unique antiviral response to eliminate the virus. This work also suggests direct roles for autophagy receptors in other lysosomal degradation pathways than canonical autophagy.
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Affiliation(s)
- Shuzhi Cui
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Tian Xia
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
- Institut Pasteur, Université Paris Cité, 28 rue du Dr. Roux, 75015, Paris, France
| | - Jianjin Zhao
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Xiaoyu Ren
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Tingtao Wu
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Mireille Kameni
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Xiaoju Guo
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Li He
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Jingao Guo
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | | | - Florence Levillayer
- Institut Pasteur, Université Paris Cité, 28 rue du Dr. Roux, 75015, Paris, France
| | - Jean-Marc Collard
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
- Institut Pasteur, Université Paris Cité, 28 rue du Dr. Roux, 75015, Paris, France
| | - Jin Zhong
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Lifeng Pan
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, 200032, Shanghai, China
| | - Frédéric Tangy
- Institut Pasteur, Université Paris Cité, 28 rue du Dr. Roux, 75015, Paris, France
| | - Pierre-Olivier Vidalain
- Institut Pasteur, Université Paris Cité, 28 rue du Dr. Roux, 75015, Paris, France
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, CNRS UMR5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007, Lyon, France
| | - Dongming Zhou
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Yaming Jiu
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Mathias Faure
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, CNRS UMR5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007, Lyon, France
| | - Yu Wei
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China.
- Institut Pasteur, Université Paris Cité, 28 rue du Dr. Roux, 75015, Paris, France.
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Tu T, Shi Y, Zhou B, Wang X, Zhang W, Zhou G, Mo X, Wang W, Wu J, Liu W. Type I collagen and fibromodulin enhance the tenogenic phenotype of hASCs and their potential for tendon regeneration. NPJ Regen Med 2023; 8:67. [PMID: 38092758 PMCID: PMC10719373 DOI: 10.1038/s41536-023-00341-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 11/09/2023] [Indexed: 12/17/2023] Open
Abstract
Our previous work demonstrated the tendon-derived extracellular matrix (ECM) extracts as vital niches to specifically direct mesenchymal stem cells towards tenogenic differentiation. This study aims to further define the effective ECM molecules capable of teno-lineage induction on human adipose-derived stem cells (hASCs) and test their function for tendon engineering. By detecting the teno-markers expression levels in hASCs exposed to various substrate coatings, collagen I (COL1) and fibromodulin (FMOD) were identified to be the key molecules as a combination and further employed to the modification of poly(L-lactide-co-ε-caprolactone) electrospun nanoyarns, which showed advantages in inducting seeded hASCs for teno-lineage specific differentiation. Under dynamic mechanical loading, modified scaffold seeded with hASCs formed neo-tendon in vitro at the histological level and formed better tendon tissue in vivo with mature histology and enhanced mechanical properties. Primary mechanistic investigation with RNA sequencing demonstrated that the inductive mechanism of these two molecules for hASCs tenogenic differentiation was directly correlated with positive regulation of peptidase activity, regulation of cell-substrate adhesion and regulation of cytoskeletal organization. These biological processes were potentially affected by LOC101929398/has-miR-197-3p/TENM4 ceRNA regulation axis. In summary, COL1 and FMOD in combination are the major bioactive molecules in tendon ECM for likely directing tenogenic phenotype of hASCs and certainly valuable for hASCs-based tendon engineering.
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Affiliation(s)
- Tian Tu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Plastic and Aesthetic Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310003, China
| | - Yuan Shi
- Department of Burn and Plastic Surgery, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215000, China
| | - Boya Zhou
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Xiaoyu Wang
- Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai, 201620, P. R. China
| | - Wenjie Zhang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- National Tissue Engineering Center of China, Shanghai, 200241, China
| | - Guangdong Zhou
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- National Tissue Engineering Center of China, Shanghai, 200241, China
| | - Xiumei Mo
- Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai, 201620, P. R. China
| | - Wenbo Wang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
| | - Jinglei Wu
- Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai, 201620, P. R. China.
| | - Wei Liu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
- National Tissue Engineering Center of China, Shanghai, 200241, China.
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