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Guo ZK, Zhang YT, Zhang Y, Weng YL, Li HY, Wu SY. [Microglia differential genes and their functions in paraquat-induced Parkinson's disease-like in mice's brains based on single-cell RNA sequencing]. Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi 2024; 42:248-257. [PMID: 38677987 DOI: 10.3760/cma.j.cn121094-20230524-00184] [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] [Subscribe] [Scholar Register] [Indexed: 04/29/2024]
Abstract
Objective: To analyze the differential genes and related signaling pathways of microglia subpopulations in Parkinson's disease (PD) -like mouse brains induced by paraquat (PQ) based on single-cell RNA sequencing, and provide clues to elucidate the mechanism of PQ-induced PD-like changes in the brain of animals. Methods: In September 2021, six male 6-week-old C57BL/6 mice were randomly divided into control group and experimental group (three mice in each group) . The mice were injected with saline, 10.0 mg/kg PQ intraperitoneally, once every three days, and 10 consecutive injections were used for modeling. After infection, the brains of mice were taken and 10×Genomics single-cell RNA sequencing was performed. Microglia subpopulations were screened based on gene expression characteristics, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed. The differential genes of microglia subpopulations between the experimental group and control group were further screened, and functional enrichment analysis was performed using bioinformatics tools. Mouse microglia (BV2 cells) were treated with 0, 60, 90 μmol/L PQ solution, respectively. And real-time fluorescence quantitative PCR experiments were conducted to validate the expressions of differential genes hexokinase 2 (Hk2) , ATPase H+ Transporting V0 Subunit B (Atp6v0b) and Neuregulin 1 (Nrg1) . Results: Cluster 7 and Cluster 20 were identified as microglia subpopulations based on the signature genes inositol polyphosphate-5-phosphatase d, Inpp5d (Inpp5d) and transforming growth factor beta receptor 1 (Tgfbr1) , and they reflected the microglia-activated M2 phenotype. The bioinformatics analysis showed that the characteristic genes of identified microglia subpopulations were enriched in endocytosis. In terms of molecular function, it mainly enriched in transmembrane receptor protein kinase activity and cytokine binding. The up-regulated genes of Cluster 7 were mainly enriched in lysosomal pathway, endocytosis pathway, and down-regulated genes were mainly enriched in neurodegenerative disease and other signaling pathways. The up-regulated genes of Cluster 20 were mainly enriched in signaling pathways related to PD, and down-regulated genes were mainly enriched in cyclic adenosine 3', 5'-monophosphate (cAMP) signaling pathways, neurological development, synaptic function and other signaling pathways. The results of real-time fluorescence quantitative PCR showed that the expressions of Hk2 mRNA and Atp6v0b mRNA increased and the expression of Nrg1 mRNA decreased in the 90 μmol/L PQ-treated BV2 cells compared with the 0 μmol/L, and the differences were statistically significant (P<0.05) . Conclusion: Microglia are activated in the PQ-induced PD-like mouse model and polarized toward the M2 phenotype. And their functions are associated with lysosomal (endocytosis) , synaptic functions and the regulation of PD-related pathways.
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Affiliation(s)
- Z K Guo
- School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Y T Zhang
- School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Y Zhang
- School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Y L Weng
- School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - H Y Li
- School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - S Y Wu
- School of Public Health, Fujian Medical University, Fuzhou 350122, China
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2
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Tao ZW, Shen YL, Weng YL. [A case report of Candida albicans meningitis]. Zhonghua Nei Ke Za Zhi 2024; 63:97-99. [PMID: 38186125 DOI: 10.3760/cma.j.cn112138-20231101-00280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Affiliation(s)
- Z W Tao
- Department of Infectious Disease, the First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Y L Shen
- Department of Infectious Disease, the First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Y L Weng
- Department of Infectious Disease, the First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
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Lee SM, Koo B, Carré C, Fischer A, He C, Kumar A, Liu K, Meyer KD, Ming GL, Peng J, Roignant JY, Storkebaum E, Sun S, De Pietri Tonelli D, Wang Y, Weng YL, Pulvirenti L, Shi Y, Yoon KJ, Song H. Exploring the brain epitranscriptome: perspectives from the NSAS summit. Front Neurosci 2023; 17:1291446. [PMID: 37928731 PMCID: PMC10625424 DOI: 10.3389/fnins.2023.1291446] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023] Open
Abstract
Increasing evidence reinforces the essential function of RNA modifications in development and diseases, especially in the nervous system. RNA modifications impact various processes in the brain, including neurodevelopment, neurogenesis, neuroplasticity, learning and memory, neural regeneration, neurodegeneration, and brain tumorigenesis, leading to the emergence of a new field termed neuroepitranscriptomics. Deficiency in machineries modulating RNA modifications has been implicated in a range of brain disorders from microcephaly, intellectual disability, seizures, and psychiatric disorders to brain cancers such as glioblastoma. The inaugural NSAS Challenge Workshop on Brain Epitranscriptomics hosted in Crans-Montana, Switzerland in 2023 assembled a group of experts from the field, to discuss the current state of the field and provide novel translational perspectives. A summary of the discussions at the workshop is presented here to simulate broader engagement from the general neuroscience field.
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Affiliation(s)
- Sung-Min Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Stem Cell Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Bonsang Koo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Stem Cell Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Clément Carré
- Transgenerational Epigenetics & Small RNA Biology, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Sorbonne Université, Paris, France
| | - André Fischer
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Chuan He
- Department of Chemistry, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, United States
- Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, United States
| | - Ajeet Kumar
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Stem Cell Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Kathy Liu
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, United States
| | - Kate D. Meyer
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, United States
| | - Guo-li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children's Research Hospital, Danny Thomas Place, Memphis, TN, United States
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Danny Thomas Place, Memphis, TN, United States
| | - Jean-Yves Roignant
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Staudingerweg, Germany
| | - Erik Storkebaum
- Donders Institute for Brain, Cognition and Behaviour and Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Shuying Sun
- Department of Physiology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | | | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA, United States
| | - Yi-Lan Weng
- Department of Neurosurgery, Houston Methodist Neurological Institute, Houston, TX, United States
| | | | - Yanhong Shi
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Ki-Jun Yoon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Stem Cell Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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Cheng Y, Song H, Ming GL, Weng YL. Epigenetic and epitranscriptomic regulation of axon regeneration. Mol Psychiatry 2023; 28:1440-1450. [PMID: 36922674 PMCID: PMC10650481 DOI: 10.1038/s41380-023-02028-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/18/2023]
Abstract
Effective axonal regeneration in the adult mammalian nervous system requires coordination of elevated intrinsic growth capacity and decreased responses to the inhibitory environment. Intrinsic regenerative capacity largely depends on the gene regulatory network and protein translation machinery. A failure to activate these pathways upon injury is underlying a lack of robust axon regeneration in the mature mammalian central nervous system. Epigenetics and epitranscriptomics are key regulatory mechanisms that shape gene expression and protein translation. Here, we provide an overview of different types of modifications on DNA, histones, and RNA, underpinning the regenerative competence of axons in the mature mammalian peripheral and central nervous systems. We highlight other non-neuronal cells and their epigenetic changes in determining the microenvironment for tissue repair and axon regeneration. We also address advancements of single-cell technology in charting transcriptomic and epigenetic landscapes that may further facilitate the mechanistic understanding of differential regenerative capacity in neuronal subtypes. Finally, as epigenetic and epitranscriptomic processes are commonly affected by brain injuries and psychiatric disorders, understanding their alterations upon brain injury would provide unprecedented mechanistic insights into etiology of injury-associated-psychiatric disorders and facilitate the development of therapeutic interventions to restore brain function.
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Affiliation(s)
- Yating Cheng
- Department of Neurosurgery, Houston Methodist Neurological Institute, Houston, TX, 77030, USA
- Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX, 77030, USA
| | - Hongjun Song
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Guo-Li Ming
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Yi-Lan Weng
- Department of Neurosurgery, Houston Methodist Neurological Institute, Houston, TX, 77030, USA.
- Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX, 77030, USA.
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5
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Hong W, Zhao Y, Weng YL, Cheng C. Random Forest model reveals the interaction between N6-methyladenosine modifications and RNA-binding proteins. iScience 2023; 26:106250. [PMID: 36922995 PMCID: PMC10009289 DOI: 10.1016/j.isci.2023.106250] [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: 07/11/2022] [Revised: 12/16/2022] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
RNA-binding proteins (RBPs) have critical roles in N6-methyladenosine (m6A) modification process. We designed a Random Forest (RF) model to systematically analyze the interaction among RBPs and m6A modifications by integrating the binding signals from hundreds of RBPs. Accurate prediction of m6A sites demonstrated significant connections between RBP bindings and m6A modifications. The relative importance of different RBPs from the model provided a quantitative metric to evaluate their interactions with m6A modifications. Redundancy analysis showed that several RBPs may have similar binding patterns with m6A sites. The RF model exhibited fairly high prediction accuracy across cell lines, suggesting a conservative RBP interaction network regulates m6A occupancy. Specific RBPs can engage to the corresponding regional m6A sites and deploy distinct regulatory processes, such as cleavage site selection of the alternative polyadenylation (APA). We also integrated histone modifications into our RF model, which demonstrated H3K36me3 and H3K27me3 as determining features for m6A distribution.
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Affiliation(s)
- Wei Hong
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yanding Zhao
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yi-Lan Weng
- Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
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Li S, Zou D, Chen W, Britz GW, Liu Z, Weng YL. METTL3 inhibition reduces N 6 -methyladenosine levels and prevents allogeneic CD4 + T-cell responses. Immunol Cell Biol 2022; 100:718-730. [PMID: 36005900 PMCID: PMC9990421 DOI: 10.1111/imcb.12581] [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: 12/10/2021] [Revised: 07/24/2022] [Accepted: 08/24/2022] [Indexed: 02/02/2023]
Abstract
Alloreactive CD4+ T cells play a central role in allograft rejection. However, the post-transcriptional regulation of the effector program in alloreactive CD4+ T cells remains unclear. N6 -methyladenosine (m6 A) RNA modification is involved in various physiological and pathological processes. Herein, we investigated whether m6 A methylation plays a role in the allogeneic T-cell effector program. m6 A levels of CD4+ T cells from spleens, draining lymph nodes and skin allografts were determined in a skin transplantation model. The effects of a METTL3 inhibitor (STM2457) on CD4+ T-cell characteristics including proliferation, cell cycle, cell apoptosis and effector differentiation were determined after stimulation of polyclonal and alloantigen-specific (TEa; CD4+ T cells specific for I-Eα52-68 ) CD4+ T cells with α-CD3/α-CD28 monoclonal antibodies and cognate CB6F1 alloantigen, respectively. We found that graft-infiltrating CD4+ T cells expressed high m6 A levels. Administration of STM2457 reduced m6 A levels, inhibited T-cell proliferation and suppressed effector differentiation of polyclonal CD4+ T cells. Alloreactive TEa cells challenged with 40 μm STM2457 exhibited deficits in T-cell proliferation and T helper type 1 cell differentiation, a cell cycle arrest in the G0 phase and elevated cell apoptosis. Moreover, these impaired T-cell responses were associated with the diminished expression levels of transcription factors Ki-67, c-Myc and T-bet. Therefore, METTL3 inhibition reduces the expression of several key transcriptional factors for the T-cell effector program and suppresses alloreactive CD4+ T-cell effector function and differentiation. Targeting m6 A-related enzymes and molecular machinery in CD4+ T cells represents an attractive therapeutic approach to prevent allograft rejection.
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Affiliation(s)
- Shuang Li
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Changsha, China
- Department of Neurosurgery, Houston Methodist Neurological Institute, Houston, Texas, USA
- Center for Neuroregeneration, Houston Methodist Research Institute, Houston, Texas, USA
| | - Dawei Zou
- Department of Surgery, Immunobiology & Transplant Science Center, Houston Methodist Research Institute and Institute for Academic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Wenhao Chen
- Department of Surgery, Immunobiology & Transplant Science Center, Houston Methodist Research Institute and Institute for Academic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Gavin W Britz
- Department of Neurosurgery, Houston Methodist Neurological Institute, Houston, Texas, USA
- Center for Neuroregeneration, Houston Methodist Research Institute, Houston, Texas, USA
| | - Zhaoqian Liu
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Yi-Lan Weng
- Department of Neurosurgery, Houston Methodist Neurological Institute, Houston, Texas, USA
- Center for Neuroregeneration, Houston Methodist Research Institute, Houston, Texas, USA
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7
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Li S, Zou D, Chen W, Cheng Y, Britz GW, Weng YL, Liu Z. Ablation of BATF Alleviates Transplant Rejection via Abrogating the Effector Differentiation and Memory Responses of CD8 + T Cells. Front Immunol 2022; 13:882721. [PMID: 35514970 PMCID: PMC9062028 DOI: 10.3389/fimmu.2022.882721] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 03/25/2022] [Indexed: 02/02/2023] Open
Abstract
Allogeneic CD8+ T cells are prominently involved in allograft rejection, but how their effector differentiation and function are regulated at a transcriptional level is not fully understood. Herein, we identified the basic leucine zipper ATF-like transcription factor (BATF) as a key transcription factor that drives the effector program of allogeneic CD8+ T cells. We found that BATF is highly expressed in graft-infiltrating CD8+ T cells, and its ablation in CD8+ T cells significantly prolonged skin allograft survival in a fully MHC-mismatched transplantation model. To investigate how BATF dictates allogeneic CD8+ T cell response, BATF-/- and wild-type (WT) CD8+ T cells were mixed in a 1:1 ratio and adoptively transferred into B6.Rag1-/- mice 1 day prior to skin transplantation. Compared with WT CD8+ T cells at the peak of rejection response, BATF-/- CD8+ T cells displayed a dysfunctional phenotype, evident by their failure to differentiate into CD127-KLRG1+ terminal effectors, impaired proliferative capacity and production of pro-inflammatory cytokines/cytotoxic molecules, and diminished capacity to infiltrate allografts. In association with the failure of effector differentiation, BATF-/- CD8+ T cells largely retained TCF1 expression and expressed significantly low levels of T-bet, TOX, and Ki67. At the memory phase, BATF-deficient CD8+ T cells displayed impaired effector differentiation upon allogeneic antigen re-stimulation. Therefore, BATF is a critical transcriptional determinant that governs the terminal differentiation and memory responses of allogeneic CD8+ T cells in the transplantation setting. Targeting BATF in CD8+ T cells may be an attractive therapeutic approach to promote transplant acceptance.
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Affiliation(s)
- Shuang Li
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China,Institute of Clinical Pharmacology, Central South University, Changsha, China,Department of Neurosurgery, Houston Methodist Neurological Institute, Houston, TX, United States,Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX, United States
| | - Dawei Zou
- Immunobiology & Transplant Science Center, Department of Surgery, Houston Methodist Research Institute & Institute for Academic Medicine, Houston Methodist Hospital, Houston, TX, United States
| | - Wenhao Chen
- Immunobiology & Transplant Science Center, Department of Surgery, Houston Methodist Research Institute & Institute for Academic Medicine, Houston Methodist Hospital, Houston, TX, United States
| | - Yating Cheng
- Department of Neurosurgery, Houston Methodist Neurological Institute, Houston, TX, United States,Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX, United States
| | - Gavin W. Britz
- Department of Neurosurgery, Houston Methodist Neurological Institute, Houston, TX, United States,Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX, United States
| | - Yi-Lan Weng
- Department of Neurosurgery, Houston Methodist Neurological Institute, Houston, TX, United States,Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX, United States,*Correspondence: Zhaoqian Liu, ;Yi-Lan Weng,
| | - Zhaoqian Liu
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China,Institute of Clinical Pharmacology, Central South University, Changsha, China,*Correspondence: Zhaoqian Liu, ;Yi-Lan Weng,
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8
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Cheng C, Zhao Y, Schaafsma E, Weng YL, Amos C. An EGFR signature predicts cell line and patient sensitivity to multiple tyrosine kinase inhibitors. Int J Cancer 2020; 147:2621-2633. [PMID: 32406930 DOI: 10.1002/ijc.33053] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 04/23/2020] [Accepted: 04/28/2020] [Indexed: 12/19/2022]
Abstract
EGFR is an oncogene with a high frequency of activating mutations in nonsmall cell lung cancer (NSCLC). EGFR inhibitors have been FDA-approved for NSCLC and have shown efficacy in patients with certain EGFR mutations. However, only 9% to 26% of these patients achieve objective responses. In our study, we developed an EGFR gene signature based on The Cancer Genome Atlas (TCGA) RNA-seq data of lung adenocarcinoma (LUAD) to direct the preselection of patients for more effective EGFR-targeted therapy. This signature infers baseline EGFR signaling pathway activity (denoted as EGFR score) in tumor samples, which is associated with tumor sensitivity to EGFR inhibitors and other tyrosine kinase inhibitors (TKIs). EGFR score predicted sensitivity of lung cancer cell lines to Erlotinib, Gefitinib and Sorafenib. Importantly, EGFR score calculated from pretreated samples was associated with patient response to Gefitinib and Sorafenib in lung cancer. Additionally, integration of the EGFR signature with TCGA LUAD data showed that it accurately predicted functional effects of different somatic EGFR mutations, and identified other mutations affecting EGFR pathway activity. Finally, using cancer cell line and clinical trial data, the EGFR score was associated with patient response to TKIs in liver cancer and other cancer types. The EGFR signature provides a useful biomarker that can expand the application of EGFR inhibitors or other TKIs and improve their treatment efficacy through patient stratification.
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Affiliation(s)
- Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA.,The Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, USA.,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Yanding Zhao
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Evelien Schaafsma
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Yi-Lan Weng
- Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, Texas, USA
| | - Christopher Amos
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA.,The Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, USA.,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
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Xu H, Dzhashiashvili Y, Shah A, Kunjamma RB, Weng YL, Elbaz B, Fei Q, Jones JS, Li YI, Zhuang X, Ming GL, He C, Popko B. m 6A mRNA Methylation Is Essential for Oligodendrocyte Maturation and CNS Myelination. Neuron 2019; 105:293-309.e5. [PMID: 31901304 DOI: 10.1016/j.neuron.2019.12.013] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 10/15/2019] [Accepted: 12/09/2019] [Indexed: 12/21/2022]
Abstract
The molecular mechanisms that govern the maturation of oligodendrocyte lineage cells remain unclear. Emerging studies have shown that N6-methyladenosine (m6A), the most common internal RNA modification of mammalian mRNA, plays a critical role in various developmental processes. Here, we demonstrate that oligodendrocyte lineage progression is accompanied by dynamic changes in m6A modification on numerous transcripts. In vivo conditional inactivation of an essential m6A writer component, METTL14, results in decreased oligodendrocyte numbers and CNS hypomyelination, although oligodendrocyte precursor cell (OPC) numbers are normal. In vitro Mettl14 ablation disrupts postmitotic oligodendrocyte maturation and has distinct effects on OPC and oligodendrocyte transcriptomes. Moreover, the loss of Mettl14 in oligodendrocyte lineage cells causes aberrant splicing of myriad RNA transcripts, including those that encode the essential paranodal component neurofascin 155 (NF155). Together, our findings indicate that dynamic RNA methylation plays an important regulatory role in oligodendrocyte development and CNS myelination.
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Affiliation(s)
- Huan Xu
- Center for Peripheral Neuropathy and Department of Neurology, University of Chicago, Chicago, IL 60637, USA
| | - Yulia Dzhashiashvili
- Center for Peripheral Neuropathy and Department of Neurology, University of Chicago, Chicago, IL 60637, USA
| | - Ankeeta Shah
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL 60637, USA; Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Rejani B Kunjamma
- Center for Peripheral Neuropathy and Department of Neurology, University of Chicago, Chicago, IL 60637, USA
| | - Yi-Lan Weng
- Department of Neuroscience and Mahoney Institute for Neurosciences, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benayahu Elbaz
- Center for Peripheral Neuropathy and Department of Neurology, University of Chicago, Chicago, IL 60637, USA
| | - Qili Fei
- Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
| | - Joshua S Jones
- Center for Peripheral Neuropathy and Department of Neurology, University of Chicago, Chicago, IL 60637, USA
| | - Yang I Li
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Xiaoxi Zhuang
- Department of Neurobiology, University of Chicago, Chicago, IL 60637, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
| | - Brian Popko
- Center for Peripheral Neuropathy and Department of Neurology, University of Chicago, Chicago, IL 60637, USA.
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10
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Weng YL, Wang X, An R, Cassin J, Vissers C, Liu Y, Liu Y, Xu T, Wang X, Wong SZH, Joseph J, Dore LC, Dong Q, Zheng W, Jin P, Wu H, Shen B, Zhuang X, He C, Liu K, Song H, Ming GL. Epitranscriptomic m 6A Regulation of Axon Regeneration in the Adult Mammalian Nervous System. Neuron 2019; 97:313-325.e6. [PMID: 29346752 DOI: 10.1016/j.neuron.2017.12.036] [Citation(s) in RCA: 253] [Impact Index Per Article: 50.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 11/05/2017] [Accepted: 12/22/2017] [Indexed: 02/07/2023]
Abstract
N6-methyladenosine (m6A) affects multiple aspects of mRNA metabolism and regulates developmental transitions by promoting mRNA decay. Little is known about the role of m6A in the adult mammalian nervous system. Here we report that sciatic nerve lesion elevates levels of m6A-tagged transcripts encoding many regeneration-associated genes and protein translation machinery components in the adult mouse dorsal root ganglion (DRG). Single-base resolution m6A-CLIP mapping further reveals a dynamic m6A landscape in the adult DRG upon injury. Loss of either m6A methyltransferase complex component Mettl14 or m6A-binding protein Ythdf1 globally attenuates injury-induced protein translation in adult DRGs and reduces functional axon regeneration in the peripheral nervous system in vivo. Furthermore, Pten deletion-induced axon regeneration of retinal ganglion neurons in the adult central nervous system is attenuated upon Mettl14 knockdown. Our study reveals a critical epitranscriptomic mechanism in promoting injury-induced protein synthesis and axon regeneration in the adult mammalian nervous system.
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Affiliation(s)
- Yi-Lan Weng
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xu Wang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Ran An
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, State Key Laboratory of Medical Neurobiology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Jessica Cassin
- Human Genetic Pre-graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Caroline Vissers
- Biochemistry, Cellular, and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yuanyuan Liu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Yajing Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Tianlei Xu
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Xinyuan Wang
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; School of Basic Medical Sciences, Fudan University, Shanghai 200040, China
| | - Samuel Zheng Hao Wong
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jessica Joseph
- Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Louis C Dore
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA; Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA
| | - Qiang Dong
- Department of Neurology, State Key Laboratory of Medical Neurobiology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Wei Zheng
- National Center for Advancing Translational Sciences, NIH, Bethesda, MD 20892, USA
| | - Peng Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Xiaoxi Zhuang
- Department of Neurobiology, University of Chicago, Chicago, IL 60637, USA
| | - Chuan He
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA; Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA
| | - Kai Liu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Hongjun Song
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Human Genetic Pre-graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Biochemistry, Cellular, and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Guo-Li Ming
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry, Cellular, and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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11
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Shi H, Zhang X, Weng YL, Lu Z, Liu Y, Lu Z, Li J, Hao P, Zhang Y, Zhang F, Wu Y, Delgado JY, Su Y, Patel MJ, Cao X, Shen B, Huang X, Ming GL, Zhuang X, Song H, He C, Zhou T. m 6A facilitates hippocampus-dependent learning and memory through YTHDF1. Nature 2018; 563:249-253. [PMID: 30401835 PMCID: PMC6226095 DOI: 10.1038/s41586-018-0666-1] [Citation(s) in RCA: 306] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 08/21/2018] [Indexed: 01/08/2023]
Abstract
N6-methyladenosine (m6A), the most prevalent internal RNA modification on mammalian messenger RNAs (mRNAs), regulates fates and functions of modified transcripts through m6A-specific binding proteins1–5. m6A is abundant in the nervous system and modulates various neural functions6–11. While m6A marks groups of mRNAs for coordinated degradation in various physiological processes12–15, the relevance of m6A in mRNA translation remains largely unknown in vivo. Here we show that, through its binding protein Ythdf1, m6A promotes protein synthesis of target transcripts in response to neuronal stimuli in the adult mouse hippocampus, thereby facilitating learning and memory. Mice with genetic deletion of Ythdf1 (Ythdf1-KO) exhibit learning and memory defects as well as impaired hippocampal synaptic transmission and long-term potentiation. Ythdf1 re-expression in the hippocampus of adult Ythdf1-KO mice rescues behavioral and synaptic defects, while hippocampus-specific acute knockdown of Ythdf1 or Mettl3, the catalytic component of m6A methyltransferase complex, recapitulates the hippocampal deficiency. Transcriptome-wide mapping of Ythdf1 binding sites and m6A sites on hippocampal mRNAs uncovered key neuronal genes. Nascent protein labeling and tether reporter assays in hippocampal neurons revealed that Ythdf1 enhances protein synthesis in a neuronal-stimulus-dependent manner. Collectively, our results uncover a pathway of mRNA m6A methylation in learning and memory, which is mediated through Ythdf1 in response to stimuli.
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Affiliation(s)
- Hailing Shi
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Xuliang Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,Laboratory Animal Center, Zhejiang University, Hangzhou, China
| | - Yi-Lan Weng
- Department of Neuroscience Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zongyang Lu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yajing Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zhike Lu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Jianan Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Piliang Hao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yu Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Feng Zhang
- Department of Neuroscience Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - You Wu
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jary Y Delgado
- Department of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Yijing Su
- Department of Neuroscience Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Meera J Patel
- Department of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Xiaohua Cao
- Key Laboratory of Brain Functional Genomics, Ministry of Education, Shanghai Key Laboratory of Brain Functional Genomics, School of Life Sciences, East China Normal University, Shanghai, China
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Guo-Li Ming
- Department of Neuroscience Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xiaoxi Zhuang
- Department of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Hongjun Song
- Department of Neuroscience Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, USA. .,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA. .,Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA. .,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
| | - Tao Zhou
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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12
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Zhang XY, Liang MJ, Liu JH, Li XH, Zhen YQ, Weng YL. [The effection of white matter abnormality to auditory and speech rehabilitation after cochlear implantation in prelingual deafness children]. Lin Chung Er Bi Yan Hou Tou Jing Wai Ke Za Zhi 2018; 31:592-597. [PMID: 29871321 DOI: 10.13201/j.issn.1001-1781.2017.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Indexed: 11/12/2022]
Abstract
Objective:To investigatethe effection of white matter abnormality to auditory and speech rehabilitation after cochlear implantation in prelingual deafness children.Method:Thirty-five children with white matter abnormality were included in this study. The degree of leukoaraiosis was evaluated by Scheltens scale based on MRI.The hearing and speechrecovery level was rated by auditory behavior grading standards(CAP) and speech intelligibility grading standards(SIR) at 6 months, 12 months, and 24 months post operation. Result:The CAP scores and SIR scores of the children with white matter abnormality were lower than those of the control group at 6 months after operation (P<0.05).The SIR scores of the children with white matter abnormality at 12 months and 24 months post operation were significantly lower than those of the control group.There was no statistically significant difference between the CAP scores of the two groups at 12 and 24 months after operation(P>0.05).Schelten classification had a greater impact on SIR scores than on CAP scores. Conclusion:The effect of white matter abnormality on auditory and speech rehabilitation after cochlear implantation was related to the degree of leukoencephalopathy. When the lesion of white matter abnormality was larger, the level of hearing and verbal rehabilitation was lower, and the speech rehabilitation was more significantly impacted by white matter lesions degree.
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Affiliation(s)
- X Y Zhang
- Department of Otolaryngology, Institute of Hearing and Speech-Language Science,Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120,China
| | - M J Liang
- Department of Otolaryngology, Institute of Hearing and Speech-Language Science,Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120,China
| | - J H Liu
- Department of Otolaryngology, Institute of Hearing and Speech-Language Science,Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120,China
| | - X H Li
- Department of Otolaryngology, Institute of Hearing and Speech-Language Science,Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120,China
| | - Y Q Zhen
- Department of Otolaryngology, Institute of Hearing and Speech-Language Science,Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120,China
| | - Y L Weng
- Department of Neurosurgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University
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13
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Weng YL, An R, Cassin J, Joseph J, Mi R, Wang C, Zhong C, Jin SG, Pfeifer GP, Bellacosa A, Dong X, Hoke A, He Z, Song H, Ming GL. An Intrinsic Epigenetic Barrier for Functional Axon Regeneration. Neuron 2017; 94:337-346.e6. [PMID: 28426967 PMCID: PMC6007997 DOI: 10.1016/j.neuron.2017.03.034] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [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: 09/24/2016] [Revised: 02/05/2017] [Accepted: 03/23/2017] [Indexed: 12/15/2022]
Abstract
Mature neurons in the adult peripheral nervous system can effectively switch from a dormant state with little axonal growth to robust axon regeneration upon injury. The mechanisms by which injury unlocks mature neurons' intrinsic axonal growth competence are not well understood. Here, we show that peripheral sciatic nerve lesion in adult mice leads to elevated levels of Tet3 and 5-hydroxylmethylcytosine in dorsal root ganglion (DRG) neurons. Functionally, Tet3 is required for robust axon regeneration of DRG neurons and behavioral recovery. Mechanistically, peripheral nerve injury induces DNA demethylation and upregulation of multiple regeneration-associated genes in a Tet3- and thymine DNA glycosylase-dependent fashion in DRG neurons. In addition, Pten deletion-induced axon regeneration of retinal ganglion neurons in the adult CNS is attenuated upon Tet1 knockdown. Together, our study suggests an epigenetic barrier that can be removed by active DNA demethylation to permit axon regeneration in the adult mammalian nervous system.
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Affiliation(s)
- Yi-Lan Weng
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ran An
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai 200040, China
| | - Jessica Cassin
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Pre-doctoral Human Genetics Training Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jessica Joseph
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ruifa Mi
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Chen Wang
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Chun Zhong
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Seung-Gi Jin
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Gerd P. Pfeifer
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Alfonso Bellacosa
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Xinzhong Dong
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ahmet Hoke
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Zhigang He
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Hongjun Song
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Pre-doctoral Human Genetics Training Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Guo-li Ming
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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14
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Abstract
The intrinsic growth capacity of neurons in the CNS declines during neuronal maturation, while neurons in the adult PNS are capable of regeneration. Injured mature PNS neurons require activation of an array of regeneration-associated genes to regain axonal growth competence. Accumulating evidence indicates a pivotal role of epigenetic mechanisms in transcriptional reprogramming and regulation of neuronal growth ability upon injury. In this review, we summarize the latest findings implicating epigenetic mechanisms, including histone and DNA modifications, in axon regeneration and discuss differential epigenomic configurations between neurons in the adult mammalian CNS and PNS.
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Affiliation(s)
- Yi-Lan Weng
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jessica Joseph
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Graduate Program in Cellular & Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ran An
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hongjun Song
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Graduate Program in Cellular & Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,The Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Guo-Li Ming
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Graduate Program in Cellular & Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,The Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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15
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Abstract
Mounting evidence has recently underscored the importance of DNA methylation in normal brain functions. DNA methylation machineries are responsible for dynamic regulation of methylation patterns in discrete brain regions. In addition to methylation of cytosines in genomic DNA (5-methylcytosine; 5mC), other forms of modified cytosines, such as 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine, can potentially act as epigenetic marks that regulate gene expression. Importantly, epigenetic modifications require cognate binding proteins to read and translate information into gene expression regulation. Abnormal or incorrect interpretation of DNA methylation patterns can cause devastating consequences, including mental illnesses and neurological disorders. Although DNA methylation was generally considered to be a stable epigenetic mark in post-mitotic cells, recent studies have revealed dynamic DNA modifications in neurons. Such reversibility of 5mC sheds light on potential mechanisms underlying some neurological disorders and suggests a new route to correct aberrant methylation patterns associated with these disorders.
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Affiliation(s)
- Yi-Lan Weng
- />Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- />Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Ran An
- />Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- />Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Jaehoon Shin
- />Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- />Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Hongjun Song
- />Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- />Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD USA
- />Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
- />The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Guo-li Ming
- />Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- />Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD USA
- />Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
- />The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD USA
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16
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Pang TL, Chen FC, Weng YL, Liao HC, Yi YH, Ho CL, Lin CH, Chen MY. Costars, a Dictyostelium protein similar to the C-terminal domain of STARS, regulates the actin cytoskeleton and motility. J Cell Sci 2010; 123:3745-55. [PMID: 20940261 DOI: 10.1242/jcs.064709] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Through analysis of a chemotaxis mutant obtained from a genetic screen in Dictyostelium discoideum, we have identified a new gene involved in regulating cell migration and have named it costars (cosA). The 82 amino acid Costars protein sequence appears highly conserved among diverse species, and significantly resembles the C-terminal region of the striated muscle activator of Rho signaling (STARS), a mammalian protein that regulates the serum response factor transcriptional activity through actin binding and Rho GTPase activation. The cosA-null (cosA(-)) cells formed smooth plaques on bacterial lawns, produced abnormally small fruiting bodies when developed on the non-nutrient agar and displayed reduced migration towards the cAMP source in chemotactic assays. Analysis of cell motion in cAMP gradients revealed decreased speed but wild-type-like directional persistence of cosA(-) cells, suggesting a defect in the cellular machinery for motility rather than for chemotactic orientation. Consistent with this notion, cosA(-) cells exhibited changes in the actin cytoskeleton, showing aberrant distribution of F-actin in fluorescence cell staining and an increased amount of cytoskeleton-associated actin. Excessive pseudopod formation was also noted in cosA(-) cells facing chemoattractant gradients. Expressing cosA or its human counterpart mCostars eliminated abnormalities of cosA(-) cells. Together, our results highlight a role for Costars in modulating actin dynamics and cell motility.
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Affiliation(s)
- Te-Ling Pang
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, National Yang-Ming University, Taipei 11221, Taiwan
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17
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Pang TL, Wu CJ, Chen PA, Weng YL, Chen MY. Dictyostelium gnt15 encodes a protein with similarity to LARGE and plays an essential role in development. Biochem Biophys Res Commun 2007; 360:83-9. [PMID: 17588537 DOI: 10.1016/j.bbrc.2007.06.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Accepted: 06/04/2007] [Indexed: 02/06/2023]
Abstract
LARGE is a putative glycosyltransferase found to be mutated in mice with myodystrophy or patients with congenital muscular dystrophy. By homology searches, we identified in the Dictyostelium discoideum genome four open reading frames, i.e. gnt12-15, encoding proteins with sequence similarity to LARGE. Semi-quantitative RT-PCR analysis revealed distinct temporal expression patterns of the four gnt genes throughout Dictyostelium development. To explore the gene function, we performed targeted disruptions of gnt14 and gnt15. The gnt14(-) strains showed no obvious phenotypes. However, gnt15(-) cells grew slowly, changed in morphology, and displayed a developmental phenotype arresting at early stages. Compared with the wild type, gnt15(-) cells were more adhesive and exhibited altered levels of some surface adhesion molecules. Moreover, lectin-binding analysis demonstrated that gnt15 disruption affected profiles of membrane glycoproteins. Taken together, our data suggest that Gnt15 is essential for Dictyostelium development and may have a role in modulating cell adhesion and glycosylation.
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Affiliation(s)
- Te-Ling Pang
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, National Yang-Ming University, Taipei 11221, Taiwan
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18
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Weng YL, Shang QX, Cai X, Cao YL. [Experimental study for repair of cranial defects with bone marrow stromal cells and modified alginate]. Shanghai Kou Qiang Yi Xue 2001; 10:35-8. [PMID: 14994075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
OBJECTIVE The primary aim of this investigation was to determine whether expanded BMSCs in vitro mixed with modified alginate gelatin could repair critical defects in rats without the addition of exogenous growth or bone morphogenetic factors. METHODS Bone marrow stem cells from syngeneic rats cultured in vitro and mixed with modified alginate gel to paint the cranial critical size defect. A full-thickness cranial plate defect was created without damage of dura mater. Modified alginate gelatin with or without BMSCs were painted over the cranial defects. Animals being made cranial defect but received no implant served as sham-operated controls. Craniotomy defects were divided into three groups, which included defects left unpainted (group I, n=6), defects painted with modified alginate gelatin alone (group II, n=6), and defects painted with a modified alginate mixed with BMSCs (group III, n=6). A total of 18 implant experiments were carried out, with postsurgical radiographic and histological analysis completed at 12 week. RESULTS None of the implants exhibited extrusion or infection. Radiographs showed a likely increased calcification in group III, without finally new calcification in group I and in group II. Histology showed that group I and group II were featured by thinning of the bone at the edges of the defect margins with minimal bone growth inward and dense fibrous tissue with rudimentary alginate material spanning the intervenient gap. The results demonstrated that a great amount of new bone in growth took place in BMSCs-alginate group, stemming from cranial defect edges and proceeding inward. CONCLUSION Transplantation of syngeneic BMSCs with alginate gel can serve as an example of a cell-based treatment for skeletal reformation and would be especially useful for augmenting or regenerating bone in skeletal defects. So syngeneic BMSCs with alginate gel demonstrate a potential technique to regenerate a variety of skeletal defects that occur in different clinical scenaries.
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Affiliation(s)
- Y L Weng
- Department of Oral Medicine, School of Stomatology, Ninth People's Hospital, Shanghai Second Medical University, Shanghai 200011, China
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Weng YL, Cao YL, Cai X, Ca V. [Autologous tissue engineered skin for full thickness skin replacement]. Shanghai Kou Qiang Yi Xue 2000; 9:164-7. [PMID: 15014807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
OBJECTIVE To evaluate the feasibility of regenerating or repairing damaged skin utilizing tissue engineering techniques. MATERIALS AND METHODS Yorkshire pigs were used in the study. A critical size defect of six, full thickness, 4 cm in diameter round wounds, which were marked on the paravertebral region of the animal were excised. The skin defects were randomly divided into three groups. Group I as control group received no cells or polymer. Group II as a second control group received pluronic hydrogel with no cells. Group III as the experimental group received a mixture of cells (keratinocytes and fibroblasts) and pluronic hydrogel. All specimens were harvested at 4 and 6 weeks in vivo, and underwent gross, histological, and transmission electron microscope evaluation. RESULTS Histologically, the skin in the experimental group was similar to normal skin with stratified epidermis overlying a moderately thick collageneous dermis. The interface of the tissue was apparently demarcated by epidermal ridges and dermal papillae. The control groups showed no skin formation except for granulation with infiltrating inflammatory cells in the wound. Transmission electron microscopy showed that the basal lamina of the experimental group was well developed and attached to the extracellular matrix. CONCLUSION This finding demonstrates the successful use of tissue engineered skin with Pluronic F-127 as a cell carrier.
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Affiliation(s)
- Y L Weng
- Department of Oral Medicine, Ninth People' s Hospital,Shanghai Second Medical University, Shanghai 200011,China
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Weng YL. [The experimental study of tissue engineered mandible condyle in the shape of human]. Shanghai Kou Qiang Yi Xue 2000; 9:94-6. [PMID: 15014818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
OBJECTIVE This study evaluates the feasibility of creating a tissue engineered adult human mandible condyle composite of bone and cartilage. METHODS A polymer template formed in the shape of the human mandible condyle using a scaffold composed of polyglycolic acid (PGA) and polylactic acid (PLA) was seeded with osteoblasts isolated from a bovine periosteum suspended in calcium alginate. Chondrocytes isolated from the same calf suspended in 30% pluronic were then "painted" onto the articular surface of the scaffold and implanted into subcutaneous pockets on the dorsa of athymic mice. Animals were divided into three groups: Group I (n=6) received PGA/PLA scaffold saturated with hydrogels not containing cells. Group II (n=6) received scaffolds seeded with both cell types suspended in saline rather than hydrogels. Group III (n=6) received scaffolds seeded with both cell types suspended in hydrogel composites. Constructs were harvested after 12 weeks, and evaluated grossly and microscopically using histologic stains. RESULTS In group I, constructs formed a small mass without evidence of new bone or cartilage. In group II, constructs were small and irregular in shape. Microscopically they contained scattered islands of bone and cartilage. All specimens in group III retained their original condylar shapes and were quite firm in consistency. Microscopic evaluation revealed trabecular bone interfacing with hyaline cartilage on its articulating surface. CONCLUSION These findings demonstrate that the composites of bone and cartilage can be engineered to serve as mandibular condylar substitutes. The interdigitation of bone and cartilage at their interface is similar to the normal interface of these composite tissues seen in articulating joints.
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Affiliation(s)
- Y L Weng
- Department of Oral Medicine, School of Stomatology, Shanghai Second Medical University. Shanghai 200011, China
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Abstract
Two new cytotoxic cembranoid diterpenes, brassicolide (1) and brassicolide acetate (2); a new cytotoxic sesquiterpene, (-)-4alpha-O-acetyl-selin-11-en (3); and six cytotoxic terpenoids, (-)-selin-11-en-4alpha-ol (4), 2-hydroxynephthenol (5), nephthenol (6), cembrene A (7), epoxycembrene A (8), and (-)-beta-elemene (9), have been isolated from the Formosan soft coral Nephthea brassica. The structures of compounds 1-9 were determined by spectral, chemical, and X-ray crystallographic analysis.
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Affiliation(s)
- C Y Duh
- Department of Marine Resources, National Sun Yat-sen University, Department of Microbiology, Kaohsiung Medical College, Department of Chemistry, and National Sun Yat-sen University, Kaohsiung, Taiwan, Republic of China
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Chen YZ, Weng YL. [Experimental research on preparation of small root canals with EDTA and cirtric acid]. Shanghai Kou Qiang Yi Xue 1998; 7:67-9. [PMID: 15071668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
OBJECTIVE:To study the effects of EDTA and citric acid on small root canals so as to provide experimental basis for clinical applications.METHODS:17% EDTA and 50% citric acid are applied to Group A and Group B respectively for three days, each group having 14 extracted teeth with small root canals. The data obtained during the three days' experiment are analyzed with statistic method.RESULTS:The 14 small root canals applied with 17% EDTA solution for three days are all effective, the overall effectiveness rate being 100% and 11 small root canals show an expansion level of 4mm or over, 9 of which reachthe length required for treatment, 11 out of the 14 small root canals applied with 50% citric acid solution for three days are effective (three are not effective), the overall effectiveness rate being 78.57%. 8 small root canals show an expansion level of over 4 mm and all of them reach the length required for treatment.Based upon statistic treatment, the expansion level of small root canals of both Group A and Group B has an obvious difference (P<0.01) after the application.CONCLUSION:EDTA should be the recommended medicine for chemical preparation of small root canals.
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Affiliation(s)
- Y Z Chen
- Department of Stomatology, Shanghai Xuhui District Central Hospital. Shanghai 200031,China
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Wang XY, Weng YL, Xu X, Kong DG, Hu ZK, Wang ZM. [The causes of misdiagnosis of periapical diseases and subsequent management]. Shanghai Kou Qiang Yi Xue 1992; 1:15-7. [PMID: 15159916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Affiliation(s)
- X Y Wang
- Department of Oral Medicine, School of Stomatology, Shanghai Second Medical University. Shanghai 200011, China
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Weng YL. [Application of tricalcium phosphate in one visit root canal treatment]. Zhonghua Kou Qiang Yi Xue Za Zhi 1991; 26:87-9, 127. [PMID: 1874073] [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] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
This paper reports the successful use of tricalcium phosphate (TCP) as periapical barrier material in animal experiments and clinics. The results of animal experiments showed that TCP had good biocompatibility with periapical tissues. At 6 weeks there were osteoids deposited on the surface of TCP. At 12 weeks osteogenesis occurred around the TCP particles and combined each other closely. At 24 weeks around the periapex there were bone deposits and a tendency of apical closure. On the basis of experiments TCP was used to treat 17 chronic periapicitis in 15 patients. All cases were young permanent teeth with immature roots. It is suggested that TCP can be applied directly in chronic periapicitis with open apices of young permanent teeth. From 6 to 12 months after filling with TCP the X-rays showed that radiolucencies reduced or eliminated, bone trabecula formed and periapical lamina dura reestablished.
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Affiliation(s)
- Y L Weng
- Department of Oral Medicine, Ninth People's Hospital, Shanghai Second Medical University
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