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Yang J, Zhu X, Wang F, Chen Z, Zhang Y, Chen J, Ni H, Zhang C, Zhuge Q. SOXC Enhances NGN2-Mediated Reprogramming of Glioblastoma Cells Into Neuron-Like Cells by Modulating RhoA and RAC1/CDC42 Pathway Activity. CNS Neurosci Ther 2024; 30:e70075. [PMID: 39390804 PMCID: PMC11467166 DOI: 10.1111/cns.70075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 09/04/2024] [Accepted: 09/24/2024] [Indexed: 10/12/2024] Open
Abstract
BACKGROUND Glioblastoma represents the most frequently diagnosed malignant neoplasm within the central nervous system. Human glioblastoma cells can be phenotypically reprogrammed into neuron-like cells through the forced expression of NEUROG2 and SOXC factors. NEUROG2 serves as a pioneer factor, establishing an initial framework for this transformation. However, the specific role of SOXC factors has not been fully elucidated. METHODS In this study, we used ChIP-seq to determine the potential target gene of NGN2. RNA-seq has been used to evaluate the transcriptional change during NGN2-SOX11-mediated neuron reprogramming. Immunofluorescence was used to determine the neuron reprogramming efficacy and cell proliferation ability. ChIP-qPCR, Co-IP, and Western Blot were performed to investigate the mechanism. RESULTS Our findings reveal that SOXC factors, in contrast to their previously identified function as transcriptional activators, act as transcriptional repressors. They achieve this by recruiting TRIM28 to suppress the expression of ECT2, a RhoGEF. This suppression results in the differential regulation of RhoA, RAC1, and CDC42 activities throughout the reprogramming process. We further establish that small molecules targeting RhoA and its effectors can substitute for SOXC factors in facilitating the neuronal reprogramming of glioblastoma cells. CONCLUSION These results underscore the pivotal role of SOXC factors' transcriptional repression and illuminate one of their specific downstream targets.
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Affiliation(s)
- Jianjing Yang
- Department of NeurosurgeryThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
- Zhejiang‐US Joint Laboratory for Aging and Neurological Disease ResearchThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouChina
- Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder ResearchThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouChina
- Department of Molecular BiologyUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Hamon Center for Regenerative Science and MedicineUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Xiaohong Zhu
- Department of NeurosurgeryThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
- Zhejiang‐US Joint Laboratory for Aging and Neurological Disease ResearchThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouChina
- Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder ResearchThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouChina
| | - Fan Wang
- Department of NeurosurgeryThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
- Zhejiang‐US Joint Laboratory for Aging and Neurological Disease ResearchThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouChina
- Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder ResearchThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouChina
| | - Zhen Chen
- Department of NeurosurgeryThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
- Zhejiang‐US Joint Laboratory for Aging and Neurological Disease ResearchThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouChina
- Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder ResearchThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouChina
| | - Ying Zhang
- Department of NeurosurgeryThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
- Zhejiang‐US Joint Laboratory for Aging and Neurological Disease ResearchThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouChina
- Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder ResearchThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouChina
| | - Jiawei Chen
- Department of NeurosurgeryThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
- Zhejiang‐US Joint Laboratory for Aging and Neurological Disease ResearchThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouChina
- Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder ResearchThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouChina
| | - Haoqi Ni
- Department of NeurosurgeryThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
- Zhejiang‐US Joint Laboratory for Aging and Neurological Disease ResearchThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouChina
- Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder ResearchThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouChina
- Department of Molecular BiologyUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Hamon Center for Regenerative Science and MedicineUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Chun‐Li Zhang
- Department of Molecular BiologyUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Hamon Center for Regenerative Science and MedicineUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Qichuan Zhuge
- Department of NeurosurgeryThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
- Zhejiang‐US Joint Laboratory for Aging and Neurological Disease ResearchThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouChina
- Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder ResearchThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouChina
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Saraswathy VM, Zhou L, Mokalled MH. Single-cell analysis of innate spinal cord regeneration identifies intersecting modes of neuronal repair. Nat Commun 2024; 15:6808. [PMID: 39147780 PMCID: PMC11327264 DOI: 10.1038/s41467-024-50628-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 07/11/2024] [Indexed: 08/17/2024] Open
Abstract
Adult zebrafish have an innate ability to recover from severe spinal cord injury. Here, we report a comprehensive single nuclear RNA sequencing atlas that spans 6 weeks of regeneration. We identify cooperative roles for adult neurogenesis and neuronal plasticity during spinal cord repair. Neurogenesis of glutamatergic and GABAergic neurons restores the excitatory/inhibitory balance after injury. In addition, a transient population of injury-responsive neurons (iNeurons) show elevated plasticity 1 week post-injury. We found iNeurons are injury-surviving neurons that acquire a neuroblast-like gene expression signature after injury. CRISPR/Cas9 mutagenesis showed iNeurons are required for functional recovery and employ vesicular trafficking as an essential mechanism that underlies neuronal plasticity. This study provides a comprehensive resource of the cells and mechanisms that direct spinal cord regeneration and establishes zebrafish as a model of plasticity-driven neural repair.
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Affiliation(s)
- Vishnu Muraleedharan Saraswathy
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Lili Zhou
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Mayssa H Mokalled
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA.
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Zhang X, Duan X, Liu X. The role of kinases in peripheral nerve regeneration: mechanisms and implications. Front Neurol 2024; 15:1340845. [PMID: 38689881 PMCID: PMC11058862 DOI: 10.3389/fneur.2024.1340845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 04/02/2024] [Indexed: 05/02/2024] Open
Abstract
Peripheral nerve injury disease is a prevalent traumatic condition in current medical practice. Despite the present treatment approaches, encompassing surgical sutures, autologous nerve or allograft nerve transplantation, tissue engineering techniques, and others, an effective clinical treatment method still needs to be discovered. Exploring novel treatment methods to improve peripheral nerve regeneration requires more effort in investigating the cellular and molecular mechanisms involved. Many factors are associated with the regeneration of injured peripheral nerves, including the cross-sectional area of the injured nerve, the length of the nerve gap defect, and various cellular and molecular factors such as Schwann cells, inflammation factors, kinases, and growth factors. As crucial mediators of cellular communication, kinases exert regulatory control over numerous signaling cascades, thereby participating in various vital biological processes, including peripheral nerve regeneration after nerve injury. In this review, we examined diverse kinase classifications, distinct nerve injury types, and the intricate mechanisms involved in peripheral nerve regeneration. Then we stressed the significance of kinases in regulating autophagy, inflammatory response, apoptosis, cell cycle, oxidative processes, and other aspects in establishing conductive microenvironments for nerve tissue regeneration. Finally, we briefly discussed the functional roles of kinases in different types of cells involved in peripheral nerve regeneration.
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Affiliation(s)
- Xu Zhang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, School of Life Science, Nantong Laboratory of Development and Diseases, Medical College, Clinical Medical Research Center, Affiliated Wuxi Clinical College of Nantong University, Nantong University, Nantong, China
- Clinical Medical Research Center, Wuxi No. 2 People's Hospital, Jiangnan University Medical Center, Wuxi, China
| | - Xuchu Duan
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, School of Life Science, Nantong Laboratory of Development and Diseases, Medical College, Clinical Medical Research Center, Affiliated Wuxi Clinical College of Nantong University, Nantong University, Nantong, China
| | - Xiaoyu Liu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, School of Life Science, Nantong Laboratory of Development and Diseases, Medical College, Clinical Medical Research Center, Affiliated Wuxi Clinical College of Nantong University, Nantong University, Nantong, China
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4
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Le D, Zhang C, Liu L, Zhao M, Liang Y, Liao P, Yang F. Neuropathic pain development following nerve injury is mediated by SOX11-ARID1A-SOCS3 transcriptional regulation in the spinal cord. Mol Biol Rep 2024; 51:281. [PMID: 38324208 DOI: 10.1007/s11033-023-09183-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/19/2023] [Indexed: 02/08/2024]
Abstract
BACKGROUND Neuropathic pain, a complex condition originating from nervous system damage, remains a significant clinical challenge due to limited understanding of its underlying mechanisms. Recent research highlights the SOX11 transcription factor, known for its role in nervous system development, as a crucial player in neuropathic pain development and maintenance. This study investigates the role of the SOX11-ARID1A-SOCS3 pathway in neuropathic pain modulation within the spinal cord. METHODS AND RESULTS Using a spinal nerve ligation (SNL) model in mice, we observed a significant upregulation of Sox11 in the spinal cord dorsal horn post-injury. Intrathecal administration of Sox11 shRNA mitigated SNL-induced neuropathic pain behaviors, including mechanical allodynia and heat hyperalgesia. Further, we demonstrated that Sox11 regulates neuropathic pain via transcriptional control of ARID1A, with subsequent modulation of SOCS3 expression. Knockdown of ARID1A and SOCS3 via shRNA resulted in alleviation of Sox11-induced pain sensitization. Additionally, Sox11 overexpression led to an increase in ARID1A binding to the SOCS3 promoter, enhancing chromatin accessibility and indicating a direct regulatory relationship. These findings were further supported by in vitro luciferase reporter assays and chromatin accessibility analysis. CONCLUSIONS The SOX11-ARID1A-SOCS3 pathway plays a pivotal role in the development and maintenance of neuropathic pain. Sox11 acts as a master regulator, modulating ARID1A, which in turn influences SOCS3 expression, thereby contributing to the modulation of neuropathic pain. These findings provide a deeper understanding of the molecular mechanisms underlying neuropathic pain and highlight potential therapeutic targets for its treatment. The differential regulation of this pathway in the spinal cord and dorsal root ganglia (DRG) underscores its complexity and the need for targeted therapeutic strategies.
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Affiliation(s)
- Dongsheng Le
- Department of Pain Management, Second Affiliated Hospital of Nanchang University, No. 1, Minde Road, Nanchang, 330006, Jiangxi Province, People's Republic of China
| | - Chao Zhang
- Department of Pain Management, Second Affiliated Hospital of Nanchang University, No. 1, Minde Road, Nanchang, 330006, Jiangxi Province, People's Republic of China
| | - Li Liu
- Department of Pain Management, Second Affiliated Hospital of Nanchang University, No. 1, Minde Road, Nanchang, 330006, Jiangxi Province, People's Republic of China
| | - Mailin Zhao
- Department of Pain Management, Second Affiliated Hospital of Nanchang University, No. 1, Minde Road, Nanchang, 330006, Jiangxi Province, People's Republic of China
| | - Yingping Liang
- Department of Pain Management, Second Affiliated Hospital of Nanchang University, No. 1, Minde Road, Nanchang, 330006, Jiangxi Province, People's Republic of China
| | - Pingsheng Liao
- Department of Pain Management, Second Affiliated Hospital of Nanchang University, No. 1, Minde Road, Nanchang, 330006, Jiangxi Province, People's Republic of China
| | - Fan Yang
- Department of Pain Management, Second Affiliated Hospital of Nanchang University, No. 1, Minde Road, Nanchang, 330006, Jiangxi Province, People's Republic of China.
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5
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Janeckova L, Knotek T, Kriska J, Hermanova Z, Kirdajova D, Kubovciak J, Berkova L, Tureckova J, Camacho Garcia S, Galuskova K, Kolar M, Anderova M, Korinek V. Astrocyte-like subpopulation of NG2 glia in the adult mouse cortex exhibits characteristics of neural progenitor cells. Glia 2024; 72:245-273. [PMID: 37772368 DOI: 10.1002/glia.24471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 09/05/2023] [Accepted: 09/05/2023] [Indexed: 09/30/2023]
Abstract
Glial cells expressing neuron-glial antigen 2 (NG2), also known as oligodendrocyte progenitor cells (OPCs), play a critical role in maintaining brain health. However, their ability to differentiate after ischemic injury is poorly understood. The aim of this study was to investigate the properties and functions of NG2 glia in the ischemic brain. Using transgenic mice, we selectively labeled NG2-expressing cells and their progeny in both healthy brain and after focal cerebral ischemia (FCI). Using single-cell RNA sequencing, we classified the labeled glial cells into five distinct subpopulations based on their gene expression patterns. Additionally, we examined the membrane properties of these cells using the patch-clamp technique. Of the identified subpopulations, three were identified as OPCs, whereas the fourth subpopulation had characteristics indicative of cells likely to develop into oligodendrocytes. The fifth subpopulation of NG2 glia showed astrocytic markers and had similarities to neural progenitor cells. Interestingly, this subpopulation was present in both healthy and post-ischemic tissue; however, its gene expression profile changed after ischemia, with increased numbers of genes related to neurogenesis. Immunohistochemical analysis confirmed the temporal expression of neurogenic genes and showed an increased presence of NG2 cells positive for Purkinje cell protein-4 at the periphery of the ischemic lesion 12 days after FCI, as well as NeuN-positive NG2 cells 28 and 60 days after injury. These results suggest the potential development of neuron-like cells arising from NG2 glia in the ischemic tissue. Our study provides insights into the plasticity of NG2 glia and their capacity for neurogenesis after stroke.
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Affiliation(s)
- Lucie Janeckova
- Laboratory of Cell and Developmental Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tomas Knotek
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jan Kriska
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Zuzana Hermanova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Denisa Kirdajova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Kubovciak
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Linda Berkova
- Laboratory of Cell and Developmental Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jana Tureckova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Sara Camacho Garcia
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Katerina Galuskova
- Laboratory of Cell and Developmental Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Kolar
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Miroslava Anderova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Vladimir Korinek
- Laboratory of Cell and Developmental Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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6
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Gordon T. Brief Electrical Stimulation Promotes Recovery after Surgical Repair of Injured Peripheral Nerves. Int J Mol Sci 2024; 25:665. [PMID: 38203836 PMCID: PMC10779324 DOI: 10.3390/ijms25010665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024] Open
Abstract
Injured peripheral nerves regenerate their axons in contrast to those in the central nervous system. Yet, functional recovery after surgical repair is often disappointing. The basis for poor recovery is progressive deterioration with time and distance of the growth capacity of the neurons that lose their contact with targets (chronic axotomy) and the growth support of the chronically denervated Schwann cells (SC) in the distal nerve stumps. Nonetheless, chronically denervated atrophic muscle retains the capacity for reinnervation. Declining electrical activity of motoneurons accompanies the progressive fall in axotomized neuronal and denervated SC expression of regeneration-associated-genes and declining regenerative success. Reduced motoneuronal activity is due to the withdrawal of synaptic contacts from the soma. Exogenous neurotrophic factors that promote nerve regeneration can replace the endogenous factors whose expression declines with time. But the profuse axonal outgrowth they provoke and the difficulties in their delivery hinder their efficacy. Brief (1 h) low-frequency (20 Hz) electrical stimulation (ES) proximal to the injury site promotes the expression of endogenous growth factors and, in turn, dramatically accelerates axon outgrowth and target reinnervation. The latter ES effect has been demonstrated in both rats and humans. A conditioning ES of intact nerve days prior to nerve injury increases axonal outgrowth and regeneration rate. Thereby, this form of ES is amenable for nerve transfer surgeries and end-to-side neurorrhaphies. However, additional surgery for applying the required electrodes may be a hurdle. ES is applicable in all surgeries with excellent outcomes.
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Affiliation(s)
- Tessa Gordon
- Division of Reconstructive Surgery, Department of Surgery, University of Toronto, Toronto, ON M4G 1X8, Canada
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Tang J, Wu M, Shen J, Jiang L, Chen L, Dang B. Possible role of Sox11 in a rat model of surgical brain injury. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2024; 27:888-894. [PMID: 38800035 PMCID: PMC11127080 DOI: 10.22038/ijbms.2024.71455.15537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 09/12/2023] [Indexed: 05/29/2024]
Abstract
Objectives Sox11, one of the SoxC family members, is an important transcription factor during neural development and neurogenesis. However, there is no report about its function in neural apoptosis. This research aims to examine the function of Sox11 in surgical brain injury (SBI). Materials and Methods We used 90 Sprague-Dawley rats to develop the SBI models and the siRNA of Sox11 to study the roles of Sox11. Western blot, real-time PCR, immunofluorescence, neuron apoptosis and necrosis, brain edema, and neurological score were determined. Results The gene and protein amount of Sox11, compared with the Sham group, were increased after SBI, which reached a peak at 12 hr. In addition, following the application of siRNAs, the amount of Sox11 protein was significantly less than that in the SBI group. On the other hand, neuronal apoptosis, necrosis, and brain edema were significantly increased, while neurological scores were decreased. Conclusion These findings demonstrate the role of Sox11 following nerve injury induced by SBI. Inhibition of Sox11 with siRNA may lead to neuronal injury and cell death, aggravating secondary brain injury after SBI.
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Affiliation(s)
- Jiafeng Tang
- Department of Rehabilitation, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China
- These authors contributed equally to this work
| | - Muyao Wu
- Department of Rehabilitation, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China
- These authors contributed equally to this work
| | - Jinchao Shen
- Department of Anesthesiology, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China
| | - Lei Jiang
- Department of Rehabilitation, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China
| | - Lifen Chen
- Department of Rehabilitation, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China
| | - Baoqi Dang
- Department of Rehabilitation, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China
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Muraleedharan Saraswathy V, Zhou L, Mokalled MH. Single-cell analysis of innate spinal cord regeneration identifies intersecting modes of neuronal repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.19.541505. [PMID: 37292638 PMCID: PMC10245778 DOI: 10.1101/2023.05.19.541505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Adult zebrafish have an innate ability to recover from severe spinal cord injury. Here, we report a comprehensive single nuclear RNA sequencing atlas that spans 6 weeks of regeneration. We identify cooperative roles for adult neurogenesis and neuronal plasticity during spinal cord repair. Neurogenesis of glutamatergic and GABAergic neurons restores the excitatory/inhibitory balance after injury. In addition, transient populations of injury-responsive neurons (iNeurons) show elevated plasticity between 1 and 3 weeks post-injury. Using cross-species transcriptomics and CRISPR/Cas9 mutagenesis, we found iNeurons are injury-surviving neurons that share transcriptional similarities with a rare population of spontaneously plastic mouse neurons. iNeurons are required for functional recovery and employ vesicular trafficking as an essential mechanism that underlies neuronal plasticity. This study provides a comprehensive resource of the cells and mechanisms that direct spinal cord regeneration and establishes zebrafish as a model of plasticity-driven neural repair.
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9
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Oprescu SN, Baumann N, Chen X, Sun Q, Zhao Y, Yue F, Wang H, Kuang S. Sox11 is enriched in myogenic progenitors but dispensable for development and regeneration of the skeletal muscle. Skelet Muscle 2023; 13:15. [PMID: 37705115 PMCID: PMC10498607 DOI: 10.1186/s13395-023-00324-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/24/2023] [Indexed: 09/15/2023] Open
Abstract
Transcription factors (TFs) play key roles in regulating differentiation and function of stem cells, including muscle satellite cells (MuSCs), a resident stem cell population responsible for postnatal regeneration of the skeletal muscle. Sox11 belongs to the Sry-related HMG-box (SOX) family of TFs that play diverse roles in stem cell behavior and tissue specification. Analysis of single-cell RNA-sequencing (scRNA-seq) datasets identify a specific enrichment of Sox11 mRNA in differentiating but not quiescent MuSCs. Consistent with the scRNA-seq data, Sox11 levels increase during differentiation of murine primary myoblasts in vitro. scRNA-seq data comparing muscle regeneration in young and old mice further demonstrate that Sox11 expression is reduced in aged MuSCs. Age-related decline of Sox11 expression is associated with reduced chromatin contacts within the topologically associating domains. Unexpectedly, Myod1Cre-driven deletion of Sox11 in embryonic myoblasts has no effects on muscle development and growth, resulting in apparently healthy muscles that regenerate normally. Pax7CreER- or Rosa26CreER- driven (MuSC-specific or global) deletion of Sox11 in adult mice similarly has no effects on MuSC differentiation or muscle regeneration. These results identify Sox11 as a novel myogenic differentiation marker with reduced expression in quiescent and aged MuSCs, but the specific function of Sox11 in myogenesis remains to be elucidated.
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Affiliation(s)
- Stephanie N Oprescu
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Nick Baumann
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Xiyue Chen
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Qiang Sun
- Department of Orthopedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong; Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, Hong Kong, China
| | - Yu Zhao
- Department of Orthopedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong; Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, Hong Kong, China
| | - Feng Yue
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Huating Wang
- Department of Orthopedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong; Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, Hong Kong, China
| | - Shihuan Kuang
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA.
- Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA.
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10
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Masi M, Biundo F, Fiou A, Racchi M, Pascale A, Buoso E. The Labyrinthine Landscape of APP Processing: State of the Art and Possible Novel Soluble APP-Related Molecular Players in Traumatic Brain Injury and Neurodegeneration. Int J Mol Sci 2023; 24:ijms24076639. [PMID: 37047617 PMCID: PMC10095589 DOI: 10.3390/ijms24076639] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/21/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
Amyloid Precursor Protein (APP) and its cleavage processes have been widely investigated in the past, in particular in the context of Alzheimer’s Disease (AD). Evidence of an increased expression of APP and its amyloidogenic-related cleavage enzymes, β-secretase 1 (BACE1) and γ-secretase, at the hit axon terminals following Traumatic Brain Injury (TBI), firstly suggested a correlation between TBI and AD. Indeed, mild and severe TBI have been recognised as influential risk factors for different neurodegenerative diseases, including AD. In the present work, we describe the state of the art of APP proteolytic processing, underlining the different roles of its cleavage fragments in both physiological and pathological contexts. Considering the neuroprotective role of the soluble APP alpha (sAPPα) fragment, we hypothesised that sAPPα could modulate the expression of genes of interest for AD and TBI. Hence, we present preliminary experiments addressing sAPPα-mediated regulation of BACE1, Isthmin 2 (ISM2), Tetraspanin-3 (TSPAN3) and the Vascular Endothelial Growth Factor (VEGFA), each discussed from a biological and pharmacological point of view in AD and TBI. We finally propose a neuroprotective interaction network, in which the Receptor for Activated C Kinase 1 (RACK1) and the signalling cascade of PKCβII/nELAV/VEGF play hub roles, suggesting that vasculogenic-targeting therapies could be a feasible approach for vascular-related brain injuries typical of AD and TBI.
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Affiliation(s)
- Mirco Masi
- Computational and Chemical Biology, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy
| | - Fabrizio Biundo
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
| | - André Fiou
- Department of Drug Sciences, Pharmacology Section, University of Pavia, Via Taramelli 12/14, 27100 Pavia, Italy
| | - Marco Racchi
- Department of Drug Sciences, Pharmacology Section, University of Pavia, Via Taramelli 12/14, 27100 Pavia, Italy
| | - Alessia Pascale
- Department of Drug Sciences, Pharmacology Section, University of Pavia, Via Taramelli 12/14, 27100 Pavia, Italy
| | - Erica Buoso
- Department of Drug Sciences, Pharmacology Section, University of Pavia, Via Taramelli 12/14, 27100 Pavia, Italy
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA
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11
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Oprescu SN, Baumann N, Chen X, Sun Q, Zhao Y, Yue F, Wang H, Kuang S. Sox11 is enriched in myogenic progenitors but dispensable for development and regeneration of skeletal muscle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.30.534956. [PMID: 37034612 PMCID: PMC10081271 DOI: 10.1101/2023.03.30.534956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Transcription factors (TFs) play key roles in regulating the differentiation and function of stem cells, including muscle satellite cells (MuSCs), a resident stem cell population responsible for postnatal regeneration of the skeletal muscle. Sox11 belongs to the Sry-related HMG-box (SOX) family of TFs that play diverse roles in stem cell behavior and tissue specification. Analysis of single-cell RNA-sequencing (scRNA-seq) datasets identify a specific enrichment of Sox11 mRNA in differentiating but not quiescent MuSCs. Consistent with the scRNA-seq data, Sox11 levels increase during differentiation of murine primary myoblasts in vitro. scRNA-seq data comparing muscle regeneration in young and old mice further demonstrate that Sox11 expression is reduced in aged MuSCs. Age-related decline of Sox11 expression is associated with reduced chromatin contacts within the topologically associated domains. Unexpectedly, Myod1 Cre -driven deletion of Sox11 in embryonic myoblasts has no effects on muscle development and growth, resulting in apparently healthy muscles that regenerate normally. Pax7 CreER or Rosa26 CreER driven (MuSC-specific or global) deletion of Sox11 in adult mice similarly has no effects on MuSC differentiation or muscle regeneration. These results identify Sox11 as a novel myogenic differentiation marker with reduced expression in quiescent and aged MuSCs, but the specific function of Sox11 in myogenesis remain to be elucidated.
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12
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Lu J, Xu H, Song K, Lin Z, Cao L, Lu B, Chen Y, Zhang S. Sox11b regulates the migration and fate determination of Müller glia-derived progenitors during retina regeneration in zebrafish. Neural Regen Res 2023; 18:445-450. [PMID: 35900444 PMCID: PMC9396499 DOI: 10.4103/1673-5374.346550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The transcription factor Sox11 plays important roles in retinal neurogenesis during vertebrate eye development. However, its function in retina regeneration remains elusive. Here we report that Sox11b, a zebrafish Sox11 homolog, regulates the migration and fate determination of Müller glia-derived progenitors (MGPCs) in an adult zebrafish model of mechanical retinal injury. Following a stab injury, the expression of Sox11b was induced in proliferating MGPCs in the retina. Sox11b knockdown did not affect MGPC formation at 4 days post-injury, although the nuclear morphology and subsequent radial migration of MGPCs were altered. At 7 days post-injury, Sox11b knockdown resulted in an increased proportion of MGPCs in the inner retina and a decreased proportion of MGPCs in the outer nuclear layer, compared with controls. Furthermore, Sox11b knockdown led to reduced photoreceptor regeneration, while it increased the numbers of newborn amacrines and retinal ganglion cells. Finally, quantitative polymerase chain reaction analysis revealed that Sox11b regulated the expression of Notch signaling components in the retina, and Notch inhibition partially recapitulated the Sox11b knockdown phenotype, indicating that Notch signaling functions downstream of Sox11b. Our findings imply that Sox11b plays key roles in MGPC migration and fate determination during retina regeneration in zebrafish, which may have critical implications for future explorations of retinal repair in mammals.
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13
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Intrinsic heterogeneity in axon regeneration. Biochem Soc Trans 2022; 50:1753-1762. [DOI: 10.1042/bst20220624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 11/18/2022]
Abstract
The nervous system is composed of a variety of neurons and glial cells with different morphology and functions. In the mammalian peripheral nervous system (PNS) or the lower vertebrate central nervous system (CNS), most neurons can regenerate extensively after axotomy, while the neurons in the mammalian CNS possess only limited regenerative ability. This heterogeneity is common within and across species. The studies about the transcriptomes after nerve injury in different animal models have revealed a series of molecular and cellular events that occurred in neurons after axotomy. However, responses of various types of neurons located in different positions of individuals were different remarkably. Thus, researchers aim to find the key factors that are conducive to regeneration, so as to provide the molecular basis for solving the regeneration difficulties after CNS injury. Here we review the heterogeneity of axonal regeneration among different cell subtypes in different animal models or the same organ, emphasizing the importance of comparative studies within and across species.
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14
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Transcriptional Control of Peripheral Nerve Regeneration. Mol Neurobiol 2022; 60:329-341. [PMID: 36261692 DOI: 10.1007/s12035-022-03090-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/10/2022] [Indexed: 10/24/2022]
Abstract
Transcription factors are master regulators of various cellular processes under diverse physiological and pathological conditions. Many transcription factors that are differentially expressed after injury to peripheral nerves play important roles in nerve regeneration. Considering that rapid and timely regrowth of injured axons is a prerequisite for successful target reinnervation, here, we compile transcription factors that mediates axon elongation, including axon growth suppressor Klf4 and axon growth promoters c-Myc, Sox11, STAT3, Atf3, c-Jun, Smad1, C/EBPδ, and p53. Besides neuronal changes, Schwann cell phenotype modulation is also critical for nerve regeneration. The activation of Schwann cells at early time points post injury provides a permissive microenvironment whereas the re-differentiation of Schwann cells at later time points supports myelin sheath formation. Hence, c-Jun and Sox2, two critical drivers for Schwann cell reprogramming, as well as Krox-20 and Sox10, two essential regulators of Schwann cell myelination, are reviewed. These transcription factors may serve as promising targets for promoting the functional recovery of injured peripheral nerves.
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15
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Jacobi A, Tran NM, Yan W, Benhar I, Tian F, Schaffer R, He Z, Sanes JR. Overlapping transcriptional programs promote survival and axonal regeneration of injured retinal ganglion cells. Neuron 2022; 110:2625-2645.e7. [PMID: 35767994 PMCID: PMC9391321 DOI: 10.1016/j.neuron.2022.06.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/08/2022] [Accepted: 06/03/2022] [Indexed: 12/12/2022]
Abstract
Injured neurons in the adult mammalian central nervous system often die and seldom regenerate axons. To uncover transcriptional pathways that could ameliorate these disappointing responses, we analyzed three interventions that increase survival and regeneration of mouse retinal ganglion cells (RGCs) following optic nerve crush (ONC) injury, albeit not to a clinically useful extent. We assessed gene expression in each of 46 RGC types by single-cell transcriptomics following ONC and treatment. We also compared RGCs that regenerated with those that survived but did not regenerate. Each intervention enhanced survival of most RGC types, but type-independent axon regeneration required manipulation of multiple pathways. Distinct computational methods converged on separate sets of genes selectively expressed by RGCs likely to be dying, surviving, or regenerating. Overexpression of genes associated with the regeneration program enhanced both survival and axon regeneration in vivo, indicating that mechanistic analysis can be used to identify novel therapeutic strategies.
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Affiliation(s)
- Anne Jacobi
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Nicholas M Tran
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Wenjun Yan
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Inbal Benhar
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Feng Tian
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Rebecca Schaffer
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Zhigang He
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA.
| | - Joshua R Sanes
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
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16
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Cheng Y, Yin Y, Zhang A, Bernstein AM, Kawaguchi R, Gao K, Potter K, Gilbert HY, Ao Y, Ou J, Fricano-Kugler CJ, Goldberg JL, He Z, Woolf CJ, Sofroniew MV, Benowitz LI, Geschwind DH. Transcription factor network analysis identifies REST/NRSF as an intrinsic regulator of CNS regeneration in mice. Nat Commun 2022; 13:4418. [PMID: 35906210 PMCID: PMC9338053 DOI: 10.1038/s41467-022-31960-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 07/08/2022] [Indexed: 01/30/2023] Open
Abstract
The inability of neurons to regenerate long axons within the CNS is a major impediment to improving outcome after spinal cord injury, stroke, and other CNS insults. Recent advances have uncovered an intrinsic program that involves coordinate regulation by multiple transcription factors that can be manipulated to enhance growth in the peripheral nervous system. Here, we use a systems genomics approach to characterize regulatory relationships of regeneration-associated transcription factors, identifying RE1-Silencing Transcription Factor (REST; Neuron-Restrictive Silencer Factor, NRSF) as a predicted upstream suppressor of a pro-regenerative gene program associated with axon regeneration in the CNS. We validate our predictions using multiple paradigms, showing that mature mice bearing cell type-specific deletions of REST or expressing dominant-negative mutant REST show improved regeneration of the corticospinal tract and optic nerve after spinal cord injury and optic nerve crush, which is accompanied by upregulation of regeneration-associated genes in cortical motor neurons and retinal ganglion cells, respectively. These analyses identify a role for REST as an upstream suppressor of the intrinsic regenerative program in the CNS and demonstrate the utility of a systems biology approach involving integrative genomics and bio-informatics to prioritize hypotheses relevant to CNS repair.
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Affiliation(s)
- Yuyan Cheng
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Yuqin Yin
- Department of Neurosurgery, Boston Children's Hospital, Boston, MA, 02115, USA
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Neurosurgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Alice Zhang
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Alexander M Bernstein
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Riki Kawaguchi
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Psychiatry, Semel Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Kun Gao
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Kyra Potter
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Hui-Ya Gilbert
- Department of Neurosurgery, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Yan Ao
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jing Ou
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Catherine J Fricano-Kugler
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jeffrey L Goldberg
- Byers Eye Institute and Wu Tsai Neuroscience Institute, Stanford University, Palo Alto, CA, 94305, USA
| | - Zhigang He
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA
| | - Clifford J Woolf
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA
| | - Michael V Sofroniew
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Larry I Benowitz
- Department of Neurosurgery, Boston Children's Hospital, Boston, MA, 02115, USA.
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, 02115, USA.
- Department of Neurosurgery, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Ophthalmology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Psychiatry, Semel Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
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17
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Liu W, Liao X, Yang Y, Lin H, Yeong J, Zhou X, Shi X, Liu J. Joint dimension reduction and clustering analysis of single-cell RNA-seq and spatial transcriptomics data. Nucleic Acids Res 2022; 50:e72. [PMID: 35349708 PMCID: PMC9262606 DOI: 10.1093/nar/gkac219] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/22/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Dimension reduction and (spatial) clustering is usually performed sequentially; however, the low-dimensional embeddings estimated in the dimension-reduction step may not be relevant to the class labels inferred in the clustering step. We therefore developed a computation method, Dimension-Reduction Spatial-Clustering (DR-SC), that can simultaneously perform dimension reduction and (spatial) clustering within a unified framework. Joint analysis by DR-SC produces accurate (spatial) clustering results and ensures the effective extraction of biologically informative low-dimensional features. DR-SC is applicable to spatial clustering in spatial transcriptomics that characterizes the spatial organization of the tissue by segregating it into multiple tissue structures. Here, DR-SC relies on a latent hidden Markov random field model to encourage the spatial smoothness of the detected spatial cluster boundaries. Underlying DR-SC is an efficient expectation-maximization algorithm based on an iterative conditional mode. As such, DR-SC is scalable to large sample sizes and can optimize the spatial smoothness parameter in a data-driven manner. With comprehensive simulations and real data applications, we show that DR-SC outperforms existing clustering and spatial clustering methods: it extracts more biologically relevant features than conventional dimension reduction methods, improves clustering performance, and offers improved trajectory inference and visualization for downstream trajectory inference analyses.
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Affiliation(s)
- Wei Liu
- Academy of Statistics and Interdisciplinary Sciences, East China Normal University, Shanghai, 200062, China
- Centre for Quantitative Medicine, Health Services & Systems Research, Duke-NUS Medical School, 169857, Singapore
| | - Xu Liao
- Centre for Quantitative Medicine, Health Services & Systems Research, Duke-NUS Medical School, 169857, Singapore
| | - Yi Yang
- Centre for Quantitative Medicine, Health Services & Systems Research, Duke-NUS Medical School, 169857, Singapore
| | - Huazhen Lin
- Center of Statistical Research and School of Statistics, Southwestern University of Finance and Economics, Chengdu, 611130, China
| | - Joe Yeong
- Institute of Molecular and Cell Biology(IMCB), Agency of Science, Technology and Research(A*STAR), 138673, Singapore
- Department of Anatomical Pathology, Singapore General Hospital, 169856, Singapore
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, 48109, USA
| | - Xingjie Shi
- Academy of Statistics and Interdisciplinary Sciences, East China Normal University, Shanghai, 200062, China
- Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, School of Statistics, East China Normal University, Shanghai, 200062, China
| | - Jin Liu
- Centre for Quantitative Medicine, Health Services & Systems Research, Duke-NUS Medical School, 169857, Singapore
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18
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Reprogramming neurons for regeneration: The fountain of youth. Prog Neurobiol 2022; 214:102284. [PMID: 35533809 DOI: 10.1016/j.pneurobio.2022.102284] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/03/2022] [Accepted: 05/02/2022] [Indexed: 01/22/2023]
Abstract
Neurons in the central nervous system (CNS) are terminally differentiated cells that gradually lose their ability to support regeneration during maturation due to changes in transcriptomic and chromatin landscape. Similar transcriptomic changes also occur during development when stem cells differentiate into different types of somatic cells. Importantly, differentiated cells can be reprogrammed back to induced pluripotent stems cells (iPSCs) via global epigenetic remodeling by combined overexpression of pluripotent reprogramming factors, including Oct4, Sox2, Klf4, c-Myc, Nanog, and/or Lin28. Moreover, recent findings showed that many proneural transcription factors were able to convert non-neural somatic cells into neurons bypassing the pluripotent stage via direct reprogramming. Interestingly, many of these factors have recently been identified as key regulators of CNS neural regeneration. Recent studies indicated that these factors could rejuvenate mature CNS neurons back to a younger state through cellular state reprogramming, thus favoring regeneration. Here we will review some recent findings regarding the roles of genetic cellular state reprogramming in regulation of neural regeneration and explore the potential underlying molecular mechanisms. Moreover, by using newly emerging techniques, such as multiomics sequencing with big data analysis and Crispr-based gene editing, we will discuss future research directions focusing on better revealing cellular state reprogramming-induced remodeling of chromatin landscape and potential translational application.
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19
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Sullivan C, Lee J, Bushey W, Demers D, Dinsdale S, Lowe K, Olmeda J, Meng ID. Evidence for a phenotypic switch in corneal afferents after lacrimal gland excision. Exp Eye Res 2022; 218:109005. [PMID: 35240196 PMCID: PMC9993327 DOI: 10.1016/j.exer.2022.109005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 01/22/2022] [Accepted: 02/19/2022] [Indexed: 01/07/2023]
Abstract
Dry eye is a common cause of ocular pain. The aim of this study was to investigate corneal innervation, ongoing pain, and alterations in corneal afferent phenotypes in a mouse model of severe aqueous tear deficiency. Chronic dry eye was produced by ipsilateral excision of the extra- and intraorbital lacrimal glands in male and female mice. Tearing was measured using a phenol thread and corneal epithelial damage assessed using fluorescein. Changes in corneal ongoing ocular pain was evaluated by measuring palpebral opening ratio. Corneal axons were visualized using Nav1.8-Cre;tdTomato reporter mice. Immunohistochemistry was performed to characterize somal expression of calcitonin gene-related peptide (CGRP), the capsaicin sensitive transient receptor potential vanilloid 1 (TRPV1), and activating transcription factor-3 (ATF-3) in tracer labeled corneal neurons following lacrimal gland excision (LGE). LGE decreased tearing, created severe epithelial damage, and decreased palpebral opening, indicative of chronic ocular irritation, over the 28-day observation period. Corneal axon terminals exhibited an acute decrease in density after LGE, followed by a regenerative process over the course of 28 days that was greater in male animals. Corneal neurons expressing CGRP, TRPV1, and ATF3 increased following injury, corresponding to axonal injury and regeneration processes observed during the same period. CGRP and TRPV1 expression was notably increased in IB4-positive cells following LGE. These results indicate that dry eye-induced damage to corneal afferents can result in alterations in IB4-positive neurons that may enhance neuroprotective mechanisms to create resiliency after chronic injury.
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Affiliation(s)
- Cara Sullivan
- Center for Excellence in the Neurosciences, University of New England, Biddeford, ME, 04005, USA; Graduate Studies in Biomedical Sciences and Engineering, University of Maine, Orono, ME, 04469, USA
| | - Jun Lee
- Center for Excellence in the Neurosciences, University of New England, Biddeford, ME, 04005, USA; Department of Complete Denture Prosthodontics, School of Dentistry, Nihon University, Tokyo, 101-8310, Japan
| | - William Bushey
- Center for Excellence in the Neurosciences, University of New England, Biddeford, ME, 04005, USA; Department of Biomedical Sciences, College of Osteopathic Medicine, University of New England, Biddeford, ME, 04005, USA
| | - Danielle Demers
- Center for Excellence in the Neurosciences, University of New England, Biddeford, ME, 04005, USA
| | - Samantha Dinsdale
- Center for Excellence in the Neurosciences, University of New England, Biddeford, ME, 04005, USA
| | - Katy Lowe
- Center for Excellence in the Neurosciences, University of New England, Biddeford, ME, 04005, USA
| | - Jessica Olmeda
- Center for Excellence in the Neurosciences, University of New England, Biddeford, ME, 04005, USA
| | - Ian D Meng
- Center for Excellence in the Neurosciences, University of New England, Biddeford, ME, 04005, USA; Graduate Studies in Biomedical Sciences and Engineering, University of Maine, Orono, ME, 04469, USA; Department of Biomedical Sciences, College of Osteopathic Medicine, University of New England, Biddeford, ME, 04005, USA.
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20
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Will Cannabigerol Trigger Neuroregeneration after a Spinal Cord Injury? An In Vitro Answer from NSC-34 Scratch-Injured Cells Transcriptome. Pharmaceuticals (Basel) 2022; 15:ph15020117. [PMID: 35215230 PMCID: PMC8875351 DOI: 10.3390/ph15020117] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/12/2022] [Accepted: 01/17/2022] [Indexed: 02/07/2023] Open
Abstract
Spinal cord injury affects the lives of millions of people around the world, often causing disability and, in unfortunate circumstances, death. Rehabilitation can partly improve outcomes and only a small percentage of patients, typically the least injured, can hope to return to normal living conditions. Cannabis sativa is gaining more and more interest in recent years, even though its beneficial properties have been known for thousands of years. Cannabigerol (CBG), extracted from C. sativa, is defined as the “mother of all cannabinoids” and its properties range from anti-inflammatory to antioxidant and neuroprotection. Using NSC-34 cells to model spinal cord injury in vitro, our work evaluated the properties of CBG treatments in motor neuron regeneration. While pre-treatment can modulate oxidative stress and increase antioxidant enzyme genes, such as Tnx1, decreasing Nos1 post-treatment seems to induce regeneration genes by triggering different pathways, such as Gap43 via p53 acetylation by Ep300 and Ddit3 and Xbp1 via Bdnf signaling, along with cytoskeletal remodeling signaling genes Nrp1 and Map1b. Our results indicate CBG as a phytocompound worth further investigation in the field of neuronal regeneration.
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21
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Reverdatto S, Prasad A, Belrose JL, Zhang X, Sammons MA, Gibbs KM, Szaro BG. Developmental and Injury-induced Changes in DNA Methylation in Regenerative versus Non-regenerative Regions of the Vertebrate Central Nervous System. BMC Genomics 2022; 23:2. [PMID: 34979916 PMCID: PMC8725369 DOI: 10.1186/s12864-021-08247-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/09/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Because some of its CNS neurons (e.g., retinal ganglion cells after optic nerve crush (ONC)) regenerate axons throughout life, whereas others (e.g., hindbrain neurons after spinal cord injury (SCI)) lose this capacity as tadpoles metamorphose into frogs, the South African claw-toed frog, Xenopus laevis, offers unique opportunities for exploring differences between regenerative and non-regenerative responses to CNS injury within the same organism. An earlier, three-way RNA-seq study (frog ONC eye, tadpole SCI hindbrain, frog SCI hindbrain) identified genes that regulate chromatin accessibility among those that were differentially expressed in regenerative vs non-regenerative CNS [11]. The current study used whole genome bisulfite sequencing (WGBS) of DNA collected from these same animals at the peak period of axon regeneration to study the extent to which DNA methylation could potentially underlie differences in chromatin accessibility between regenerative and non-regenerative CNS. RESULTS Consistent with the hypothesis that DNA of regenerative CNS is more accessible than that of non-regenerative CNS, DNA from both the regenerative tadpole hindbrain and frog eye was less methylated than that of the non-regenerative frog hindbrain. Also, consistent with observations of CNS injury in mammals, DNA methylation in non-regenerative frog hindbrain decreased after SCI. However, contrary to expectations that the level of DNA methylation would decrease even further with axotomy in regenerative CNS, DNA methylation in these regions instead increased with injury. Injury-induced differences in CpG methylation in regenerative CNS became especially enriched in gene promoter regions, whereas non-CpG methylation differences were more evenly distributed across promoter regions, intergenic, and intragenic regions. In non-regenerative CNS, tissue-related (i.e., regenerative vs. non-regenerative CNS) and injury-induced decreases in promoter region CpG methylation were significantly correlated with increased RNA expression, but the injury-induced, increased CpG methylation seen in regenerative CNS across promoter regions was not, suggesting it was associated with increased rather than decreased chromatin accessibility. This hypothesis received support from observations that in regenerative CNS, many genes exhibiting increased, injury-induced, promoter-associated CpG-methylation also exhibited increased RNA expression and association with histone markers for active promoters and enhancers. DNA immunoprecipitation for 5hmC in optic nerve regeneration found that the promoter-associated increases seen in CpG methylation were distinct from those exhibiting changes in 5hmC. CONCLUSIONS Although seemingly paradoxical, the increased injury-associated DNA methylation seen in regenerative CNS has many parallels in stem cells and cancer. Thus, these axotomy-induced changes in DNA methylation in regenerative CNS provide evidence for a novel epigenetic state favoring successful over unsuccessful CNS axon regeneration. The datasets described in this study should help lay the foundations for future studies of the molecular and cellular mechanisms involved. The insights gained should, in turn, help point the way to novel therapeutic approaches for treating CNS injury in mammals.
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Affiliation(s)
- Sergei Reverdatto
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
- Center for Neuroscience Research, University at Albany, State University of New York, Albany, NY, 12222, USA
- RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Aparna Prasad
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
- Center for Neuroscience Research, University at Albany, State University of New York, Albany, NY, 12222, USA
- RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Jamie L Belrose
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
- Center for Neuroscience Research, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Xiang Zhang
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Morgan A Sammons
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
- RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Kurt M Gibbs
- Department of Biology & Chemistry, Morehead State University, Morehead, KY, 40351, USA
| | - Ben G Szaro
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA.
- Center for Neuroscience Research, University at Albany, State University of New York, Albany, NY, 12222, USA.
- RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA.
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22
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Klimovich P, Rubina K, Sysoeva V, Semina E. New Frontiers in Peripheral Nerve Regeneration: Concerns and Remedies. Int J Mol Sci 2021; 22:13380. [PMID: 34948176 PMCID: PMC8703705 DOI: 10.3390/ijms222413380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/30/2021] [Accepted: 12/07/2021] [Indexed: 01/08/2023] Open
Abstract
Topical advances in studying molecular and cellular mechanisms responsible for regeneration in the peripheral nervous system have highlighted the ability of the nervous system to repair itself. Still, serious injuries represent a challenge for the morphological and functional regeneration of peripheral nerves, calling for new treatment strategies that maximize nerve regeneration and recovery. This review presents the canonical view of the basic mechanisms of nerve regeneration and novel data on the role of exosomes and their transferred microRNAs in intracellular communication, regulation of axonal growth, Schwann cell migration and proliferation, and stromal cell functioning. An integrated comprehensive understanding of the current mechanistic underpinnings will open the venue for developing new clinical strategies to ensure full regeneration in the peripheral nervous system.
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Affiliation(s)
- Polina Klimovich
- National Cardiology Research Center Ministry of Health of the Russian Federation, Institute of Experimental Cardiology, 121552 Moscow, Russia; (P.K.); (E.S.)
- Faculty of Medicine, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Kseniya Rubina
- Faculty of Medicine, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Veronika Sysoeva
- Faculty of Medicine, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Ekaterina Semina
- National Cardiology Research Center Ministry of Health of the Russian Federation, Institute of Experimental Cardiology, 121552 Moscow, Russia; (P.K.); (E.S.)
- Faculty of Medicine, Lomonosov Moscow State University, 119991 Moscow, Russia;
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Lowell JA, O’Neill N, Danzi MC, Al-Ali H, Bixby JL, Lemmon VP. Phenotypic Screening Following Transcriptomic Deconvolution to Identify Transcription Factors Mediating Axon Growth Induced by a Kinase Inhibitor. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:1337-1354. [PMID: 34218704 PMCID: PMC10509783 DOI: 10.1177/24725552211026270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
After injury to the central nervous system (CNS), both neuron-intrinsic limitations on regenerative responses and inhibitory factors in the injured CNS environment restrict regenerative axon growth. Instances of successful axon regrowth offer opportunities to identify features that differentiate these situations from that of the normal adult CNS. One such opportunity is provided by the kinase inhibitor RO48, which dramatically enhances neurite outgrowth of neurons in vitro and substantially increased contralateral sprouting of corticospinal tract neurons when infused intraventricularly following unilateral pyramidotomy. The authors present here a transcriptomic deconvolution of RO48-associated axon growth, with the goal of identifying transcriptional regulators associated with axon growth in the CNS. Through the use of RNA sequencing (RNA-seq) and transcription factor binding site enrichment analysis, the authors identified a list of transcription factors putatively driving differential gene expression during RO48-induced neurite outgrowth of rat hippocampal neurons in vitro. The 82 transcription factor motifs identified in this way included some with known association to axon growth regulation, such as Jun, Klf4, Myc, Atf4, Stat3, and Nfatc2, and many with no known association to axon growth. A phenotypic loss-of-function screen was carried out to evaluate these transcription factors for their roles in neurite outgrowth; this screen identified several potential outgrowth regulators. Subsequent validation suggests that the Forkhead box (Fox) family transcription factor Foxp2 restricts neurite outgrowth, while FoxO subfamily members Foxo1 and Foxo3a promote neurite outgrowth. The authors' combined transcriptomic-phenotypic screening strategy therefore allowed identification of novel transcriptional regulators of neurite outgrowth downstream of a multitarget kinase inhibitor.
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Affiliation(s)
- Jeffrey A. Lowell
- Miami Project to Cure Paralysis and University of Miami Miller School of Medicine, Miami, FL, USA
| | - Nicholas O’Neill
- Miami Project to Cure Paralysis and University of Miami Miller School of Medicine, Miami, FL, USA
| | - Matt C. Danzi
- Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Hassan Al-Ali
- Miami Project to Cure Paralysis and University of Miami Miller School of Medicine, Miami, FL, USA
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL, USA
- Department of Medicine and Peggy & Harold Katz Family Drug Discovery Center, University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - John L. Bixby
- Miami Project to Cure Paralysis and University of Miami Miller School of Medicine, Miami, FL, USA
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Vance P. Lemmon
- Miami Project to Cure Paralysis and University of Miami Miller School of Medicine, Miami, FL, USA
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
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Yow YY, Goh TK, Nyiew KY, Lim LW, Phang SM, Lim SH, Ratnayeke S, Wong KH. Therapeutic Potential of Complementary and Alternative Medicines in Peripheral Nerve Regeneration: A Systematic Review. Cells 2021; 10:cells10092194. [PMID: 34571842 PMCID: PMC8472132 DOI: 10.3390/cells10092194] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022] Open
Abstract
Despite the progressive advances, current standards of treatments for peripheral nerve injury do not guarantee complete recovery. Thus, alternative therapeutic interventions should be considered. Complementary and alternative medicines (CAMs) are widely explored for their therapeutic value, but their potential use in peripheral nerve regeneration is underappreciated. The present systematic review, designed according to guidelines of Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols, aims to present and discuss the current literature on the neuroregenerative potential of CAMs, focusing on plants or herbs, mushrooms, decoctions, and their respective natural products. The available literature on CAMs associated with peripheral nerve regeneration published up to 2020 were retrieved from PubMed, Scopus, and Web of Science. According to current literature, the neuroregenerative potential of Achyranthes bidentata, Astragalus membranaceus, Curcuma longa, Panax ginseng, and Hericium erinaceus are the most widely studied. Various CAMs enhanced proliferation and migration of Schwann cells in vitro, primarily through activation of MAPK pathway and FGF-2 signaling, respectively. Animal studies demonstrated the ability of CAMs to promote peripheral nerve regeneration and functional recovery, which are partially associated with modulations of neurotrophic factors, pro-inflammatory cytokines, and anti-apoptotic signaling. This systematic review provides evidence for the potential use of CAMs in the management of peripheral nerve injury.
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Affiliation(s)
- Yoon-Yen Yow
- Department of Biological Sciences, School of Medicine and Life Sciences, Sunway University, Petaling Jaya 47500, Malaysia; (T.-K.G.); (K.-Y.N.); (S.R.)
- Correspondence: (Y.-Y.Y.); (L.-W.L.); (K.-H.W.); Tel.: +603-7491-8622 (Y.-Y.Y.); +852-3917-6830 (L.-W.L.); +603-7967-4729 (K.-H.W.)
| | - Tiong-Keat Goh
- Department of Biological Sciences, School of Medicine and Life Sciences, Sunway University, Petaling Jaya 47500, Malaysia; (T.-K.G.); (K.-Y.N.); (S.R.)
| | - Ke-Ying Nyiew
- Department of Biological Sciences, School of Medicine and Life Sciences, Sunway University, Petaling Jaya 47500, Malaysia; (T.-K.G.); (K.-Y.N.); (S.R.)
| | - Lee-Wei Lim
- Neuromodulation Laboratory, School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, L4 Laboratory Block, Hong Kong
- Correspondence: (Y.-Y.Y.); (L.-W.L.); (K.-H.W.); Tel.: +603-7491-8622 (Y.-Y.Y.); +852-3917-6830 (L.-W.L.); +603-7967-4729 (K.-H.W.)
| | - Siew-Moi Phang
- Institute of Ocean and Earth Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
- Faculty of Applied Sciences, UCSI University, Cheras, Kuala Lumpur 56000, Malaysia
| | - Siew-Huah Lim
- Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
| | - Shyamala Ratnayeke
- Department of Biological Sciences, School of Medicine and Life Sciences, Sunway University, Petaling Jaya 47500, Malaysia; (T.-K.G.); (K.-Y.N.); (S.R.)
| | - Kah-Hui Wong
- Department of Anatomy, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Correspondence: (Y.-Y.Y.); (L.-W.L.); (K.-H.W.); Tel.: +603-7491-8622 (Y.-Y.Y.); +852-3917-6830 (L.-W.L.); +603-7967-4729 (K.-H.W.)
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Wang J, Struebing FL, Geisert EE. Commonalities of optic nerve injury and glaucoma-induced neurodegeneration: Insights from transcriptome-wide studies. Exp Eye Res 2021; 207:108571. [PMID: 33844961 PMCID: PMC9890784 DOI: 10.1016/j.exer.2021.108571] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 03/28/2021] [Accepted: 04/02/2021] [Indexed: 02/03/2023]
Abstract
Glaucoma is a collection of diseases that lead to an irreversible vision loss due to damage of retinal ganglion cells (RGCs). Although the underlying events leading to RGC death are not fully understood, recent research efforts are beginning to define the genetic changes that play a critical role in the initiation and progression of glaucomatous injury and RGC death. Several genetic and experimental animal models have been developed to mimic glaucomatous neurodegeneration. These models differ in many respects but all result in the loss of RGCs. Assessing transcriptional changes across different models could provide a more complete perspective on the molecular drivers of RGC degeneration. For the past several decades, changes in the retinal transcriptome during neurodegeneration process were defined using microarray methods, RNA sequencing and now single cell RNA sequencing. It is understood that these methods have strengths and weaknesses due to technical differences and variations in the analytical tools used. In this review, we focus on the use of transcriptome-wide expression profiling of the changes occurring as RGCs are lost across different glaucoma models. Commonalities of optic nerve crush and glaucoma-induced neurodegeneration are identified and discussed.
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Affiliation(s)
- Jiaxing Wang
- Emory Eye Center, Department of Ophthalmology, Emory University, 1365B Clifton Road NE, Atlanta, GA, 30322, USA
| | - Felix L. Struebing
- Center for Neuropathology and Prion Research, Ludwig Maximilian University of Munich, Germany,Department for Translational Brain Research, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Eldon E. Geisert
- Emory Eye Center, Department of Ophthalmology, Emory University, 1365B Clifton Road NE, Atlanta, GA, 30322, USA,Corresponding author: (E.E. Geisert)
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Early Life Nociception is Influenced by Peripheral Growth Hormone Signaling. J Neurosci 2021; 41:4410-4427. [PMID: 33888610 DOI: 10.1523/jneurosci.3081-20.2021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 12/28/2022] Open
Abstract
A number of cellular systems work in concert to modulate nociceptive processing in the periphery, but the mechanisms that regulate neonatal nociception may be distinct compared with adults. Our previous work indicated a relationship between neonatal hypersensitivity and growth hormone (GH) signaling. Here, we explored the peripheral mechanisms by which GH modulated neonatal nociception under normal and injury conditions (incision) in male and female mice. We found that GH receptor (GHr) signaling in primary afferents maintains a tonic inhibition of peripheral hypersensitivity. After injury, a macrophage dependent displacement of injury-site GH was found to modulate neuronal transcription at least in part via serum response factor (SRF) regulation. A single GH injection into the injured hindpaw muscle effectively restored available GH signaling to neurons and prevented acute pain-like behaviors, primary afferent sensitization, and neuronal gene expression changes. GH treatment also inhibited long-term somatosensory changes observed after repeated peripheral insult. Results may indicate a novel mechanism of neonatal nociception.SIGNIFICANCE STATEMENT Although it is noted that mechanisms of pain development in early life are unique compared with adults, little research focuses on neonatal-specific peripheral mechanisms of nociception. This gap is evident in the lack of specialized care for infants following an injury including surgeries. This report evaluates how distinct cellular systems in the periphery including the endocrine, immune and nervous systems work together to modulate neonatal-specific nociception. We uncovered a novel mechanism by which muscle injury induces a macrophage-dependent sequestration of peripheral growth hormone (GH) that effectively removes its normal tonic inhibition of neonatal nociceptors to promote acute pain-like behaviors. Results indicate a possible new strategy for treatment of neonatal postsurgical pain.
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Abstract
OBJECTIVE Comprehensive molecular profiling of radioresistant and cystic vestibular schwannoma (VS) subtypes. STUDY DESIGN Our study utilized whole-exome sequencing (WES), RNA-sequencing (RNAseq), and correlated clinical data from 12 samples (2 samples of solid sporadic subtype, 8 with cystic changes, and 2 previously irradiated). SETTING Academic medical center. PATIENTS Patients diagnosed with VS who required surgical treatment. Inclusion: Cystic and radioresistant tumors matched to age and tumor volume, with solid sporadic VS samples as control; Exclusion: NF-2 patients. INTERVENTION(S) WES using custom probes for copy number analysis. A modified version of the Agilent Human Whole Exome sequencing hybrid capture system was used to process samples. Recurrent variants were identified and compared between groups. Leukocyte-derived DNA was utilized as internal control to reduce false-positives. MAIN OUTCOME MEASURE(S) Analysis of genetic landscape of VS subtypes (naive solid VS, cystic VS, and previously irradiated VS) by performing deep next-generation sequencing. RESULTS WES data achieved a mean coverage of 202X and RNAseq generated an average of 74 million total reads. As a group, 25% of samples had 22q loss. Somatic analysis identified previously reported genes and multiple novel mutations across samples. Differential expression analysis of RNAseq data found significantly mutated genes such as COL6A3, CLMP, ART4, Lumican that were shared by both cystic VS and irradiated VS, but not seen in sporadic VS. CONCLUSIONS Using WES we were able to demonstrate that cystic and irradiated samples are subtypes of VS with an increased mutation burden and a unique genetic fingerprint. We identified differences between the genomic and molecular profile of cystic VS and radioresistant VS. Our results help advance the understanding of the pathophysiology of these tumor subtypes and suggest possible molecular targets for novel treatment strategies.
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28
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Wheaton BJ, Sena J, Sundararajan A, Umale P, Schilkey F, Miller RD. Identification of regenerative processes in neonatal spinal cord injury in the opossum (Monodelphis domestica): A transcriptomic study. J Comp Neurol 2021; 529:969-986. [PMID: 32710567 PMCID: PMC7855507 DOI: 10.1002/cne.24994] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 12/20/2022]
Abstract
This study investigates the response to spinal cord injury in the gray short‐tailed opossum (Monodelphis domestica). In opossums spinal injury early in development results in spontaneous axon growth through the injury, but this regenerative potential diminishes with maturity until it is lost entirely. The mechanisms underlying this regeneration remain unknown. RNA sequencing was used to identify differential gene expression in regenerating (SCI at postnatal Day 7, P7SCI) and nonregenerating (SCI at Day 28, P28SCI) cords +1d, +3d, and +7d after complete spinal transection, compared to age‐matched controls. Genes showing significant differential expression (log2FC ≥ 1, Padj ≤ 0.05) were used for downstream analysis. Across all time‐points 233 genes altered expression after P7SCI, and 472 genes altered expression after P28SCI. One hundred and forty‐seven genes altered expression in both injury ages (63% of P7SCI data set). The majority of changes were gene upregulations. Gene ontology overrepresentation analysis in P7SCI gene‐sets showed significant overrepresentations only in immune‐associated categories, while P28SCI gene‐sets showed overrepresentations in these same immune categories, along with other categories such as “cell proliferation,” “cell adhesion,” and “apoptosis.” Cell‐type–association analysis suggested that, regardless of injury age, injury‐associated gene transcripts were most strongly associated with microglia and endothelial cells, with strikingly fewer astrocyte, oligodendrocyte and neuron‐related genes, the notable exception being a cluster of mostly downregulated oligodendrocyte‐associated genes in the P7SCI + 7d gene‐set. Our findings demonstrate a more complex transcriptomic response in nonregenerating cords, suggesting a strong influence of non‐neuronal cells in the outcome after injury and providing the largest survey yet of the transcriptomic changes occurring after SCI in this model.
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Affiliation(s)
- Benjamin J Wheaton
- Department of Integrative Medical Biology, University of Umeå, Umeå, Sweden.,Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Johnny Sena
- National Center for Genome Resources, Santa Fe, New Mexico, USA
| | | | - Pooja Umale
- National Center for Genome Resources, Santa Fe, New Mexico, USA
| | - Faye Schilkey
- National Center for Genome Resources, Santa Fe, New Mexico, USA
| | - Robert D Miller
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, New Mexico, USA
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29
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Renthal W, Tochitsky I, Yang L, Cheng YC, Li E, Kawaguchi R, Geschwind DH, Woolf CJ. Transcriptional Reprogramming of Distinct Peripheral Sensory Neuron Subtypes after Axonal Injury. Neuron 2020; 108:128-144.e9. [PMID: 32810432 PMCID: PMC7590250 DOI: 10.1016/j.neuron.2020.07.026] [Citation(s) in RCA: 230] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 05/27/2020] [Accepted: 07/22/2020] [Indexed: 12/27/2022]
Abstract
Primary somatosensory neurons are specialized to transmit specific types of sensory information through differences in cell size, myelination, and the expression of distinct receptors and ion channels, which together define their transcriptional and functional identity. By profiling sensory ganglia at single-cell resolution, we find that all somatosensory neuronal subtypes undergo a similar transcriptional response to peripheral nerve injury that both promotes axonal regeneration and suppresses cell identity. This transcriptional reprogramming, which is not observed in non-neuronal cells, resolves over a similar time course as target reinnervation and is associated with the restoration of original cell identity. Injury-induced transcriptional reprogramming requires ATF3, a transcription factor that is induced rapidly after injury and necessary for axonal regeneration and functional recovery. Our findings suggest that transcription factors induced early after peripheral nerve injury confer the cellular plasticity required for sensory neurons to transform into a regenerative state.
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Affiliation(s)
- William Renthal
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd., Boston, MA 02115, USA; Department of Neurobiology, Harvard Medical School, 220 Longwood Ave., Boston, MA 02115, USA.
| | - Ivan Tochitsky
- Department of Neurobiology, Harvard Medical School, 220 Longwood Ave., Boston, MA 02115, USA; F.M. Kirby Neurobiology Center, Boston Children's Hospital, 3 Blackfan Cir., Boston, MA 02115, USA
| | - Lite Yang
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd., Boston, MA 02115, USA; Department of Neurobiology, Harvard Medical School, 220 Longwood Ave., Boston, MA 02115, USA; F.M. Kirby Neurobiology Center, Boston Children's Hospital, 3 Blackfan Cir., Boston, MA 02115, USA
| | - Yung-Chih Cheng
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, 3 Blackfan Cir., Boston, MA 02115, USA
| | - Emmy Li
- Department of Neurobiology, Harvard Medical School, 220 Longwood Ave., Boston, MA 02115, USA
| | - Riki Kawaguchi
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Clifford J Woolf
- Department of Neurobiology, Harvard Medical School, 220 Longwood Ave., Boston, MA 02115, USA; F.M. Kirby Neurobiology Center, Boston Children's Hospital, 3 Blackfan Cir., Boston, MA 02115, USA.
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30
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Keller N, Mendoza-Ferreira N, Maroofian R, Chelban V, Khalil Y, Mills PB, Boostani R, Torbati PN, Karimiani EG, Thiele H, Houlden H, Wirth B, Karakaya M. Hereditary polyneuropathy with optic atrophy due to PDXK variant leading to impaired Vitamin B6 metabolism. Neuromuscul Disord 2020; 30:583-589. [DOI: 10.1016/j.nmd.2020.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/07/2020] [Accepted: 04/21/2020] [Indexed: 01/13/2023]
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Suzuki N, Ochi H. Regeneration enhancers: A clue to reactivation of developmental genes. Dev Growth Differ 2020; 62:343-354. [PMID: 32096563 PMCID: PMC7383998 DOI: 10.1111/dgd.12654] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 01/17/2020] [Accepted: 01/20/2020] [Indexed: 12/18/2022]
Abstract
During tissue and organ regeneration, cells initially detect damage and then alter nuclear transcription in favor of tissue/organ reconstruction. Until recently, studies of tissue regeneration have focused on the identification of relevant genes. These studies show that many developmental genes are reused during regeneration. Concurrently, comparative genomics studies have shown that the total number of genes does not vastly differ among vertebrate taxa. Moreover, functional analyses of developmental genes using various knockout/knockdown techniques demonstrated that the functions of these genes are conserved among vertebrates. Despite these data, the ability to regenerate damaged body parts varies widely between animals. Thus, it is important to determine how regenerative transcriptional programs are triggered and why animals with low regenerative potential fail to express developmental genes after injury. Recently, we discovered relevant enhancers and named them regeneration signal-response enhancers (RSREs) after identifying their activation mechanisms in a Xenopus laevis transgenic system. In this review, we summarize recent studies of injury/regeneration-associated enhancers and then discuss their mechanisms of activation.
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Affiliation(s)
- Nanoka Suzuki
- Amphibian Research CenterHiroshima UniversityHigashi‐HiroshimaJapan
| | - Haruki Ochi
- Institute for Promotion of Medical Science ResearchFaculty of MedicineYamagata UniversityYamagataJapan
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32
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Lin W, Xu L, Li G. Molecular Insights Into Lysyl Oxidases in Cartilage Regeneration and Rejuvenation. Front Bioeng Biotechnol 2020; 8:359. [PMID: 32426343 PMCID: PMC7204390 DOI: 10.3389/fbioe.2020.00359] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 03/31/2020] [Indexed: 12/13/2022] Open
Abstract
Articular cartilage remains among the most difficult tissues to regenerate due to its poor self-repair capacity. The lysyl oxidase family (LOX; also termed as protein-lysine 6-oxidase), mainly consists of lysyl oxidase (LO) and lysyl oxidase-like 1-4 (LOXL1-LOXL4), has been traditionally defined as cuproenzymes that are essential for stabilization of extracellular matrix, particularly cross-linking of collagen and elastin. LOX is essential in the musculoskeletal system, particularly cartilage. LOXs-mediated collagen cross-links are essential for the functional integrity of articular cartilage. Appropriate modulation of the expression or activity of certain LOX members selectively may become potential promising strategy for cartilage repair. In the current review, we summarized the advances of LOX in cartilage homeostasis and functioning, as well as copper-mediated activation of LOX through hypoxia-responsive signaling axis during recent decades. Also, the molecular signaling network governing LOX expression has been summarized, indicating that appropriate modulation of hypoxia-responsive-signaling-directed LOX expression through manipulation of bioavailability of copper and oxygen is promising for further clinical implications of cartilage regeneration, which has emerged as a potential therapeutic approach for cartilage rejuvenation in tissue engineering and regenerative medicine. Therefore, targeted regulation of copper-mediated hypoxia-responsive signalling axis for selective modulation of LOX expression may become potential effective therapeutics for enhanced cartilage regeneration and rejuvenation in future clinical implications.
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Affiliation(s)
- Weiping Lin
- Department of Orthopaedics and Traumatology, Stem Cells and Regenerative Medicine Laboratory, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Liangliang Xu
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Gang Li
- Department of Orthopaedics and Traumatology, Stem Cells and Regenerative Medicine Laboratory, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China.,MOE Key Laboratory for Regenerative Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
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Wang D, Chen Y, Liu M, Cao Q, Wang Q, Zhou S, Wang Y, Mao S, Gu X, Luo Z, Yu B. The long noncoding RNA Arrl1 inhibits neurite outgrowth by functioning as a competing endogenous RNA during neuronal regeneration in rats. J Biol Chem 2020; 295:8374-8386. [PMID: 32336677 DOI: 10.1074/jbc.ra119.011917] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 04/22/2020] [Indexed: 01/02/2023] Open
Abstract
The intrinsic regeneration ability of neurons is a pivotal factor in the repair of peripheral nerve injury. Therefore, identifying the key modulators of nerve regeneration may help improve axon regeneration and functional recovery after injury. Unlike for classical transcription factors and regeneration-associated genes, the function of long noncoding RNAs (lncRNAs) in the regulation of neuronal regeneration remains mostly unknown. In this study, we used RNA-Seq-based transcriptome profiling to analyze the expression patterns of lncRNAs and mRNAs in rat dorsal root ganglion (DRG) following sciatic nerve injury. Analyses using the lncRNA-mRNA co-expression network, gene ontology enrichment, and Kyoto Encyclopedia of Genes and Genomes pathway databases indicated that the lncRNA Arrl1 decreases neurite outgrowth after neuronal injury. shRNA-mediated Arrl1 silencing increased axon regeneration both in vitro and in vivo and improved functional recovery of the sciatic nerve. Moreover, inhibiting an identified target gene of Arrl1, cyclin-dependent kinase inhibitor 2B (Cdkn2b), markedly promoted neurite outgrowth of DRG neurons. We also found that Arrl1 acts as a competing endogenous RNA that sponges a Cdkn2b repressor, microRNA-761 (miR-761), and thereby up-regulates Cdkn2b expression during neuron regeneration. We conclude that the lncRNA Arrl1 affects the intrinsic regeneration of DRG neurons by derepressing Cdkn2b expression. Our findings indicate a role for an lncRNA-microRNA-kinase pathway in the regulation of axon regeneration and functional recovery following peripheral nerve injury in rats.
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Affiliation(s)
- Dong Wang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Yanping Chen
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Mingwen Liu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Qianqian Cao
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Qihui Wang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Shuoshuo Zhou
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Yaxian Wang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Susu Mao
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Xiaosong Gu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China.,Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Affiliated Hospital of Nantong University, Nantong University, Nantong, China
| | - Zhenge Luo
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Bin Yu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China .,Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Affiliated Hospital of Nantong University, Nantong University, Nantong, China
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Hezroni H, Perry RBT, Ulitsky I. Long Noncoding RNAs in Development and Regeneration of the Neural Lineage. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:165-177. [PMID: 31900326 DOI: 10.1101/sqb.2019.84.039347] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Long noncoding RNAs (lncRNAs) are gathering increasing attention toward their roles in different biological systems. In mammals, the richest repertoires of lncRNAs are expressed in the brain and in the testis, and the diversity of lncRNAs in the nervous system is thought to be related to the diversity and the complexity of its cell types. Supporting this notion, many lncRNAs are differentially expressed between different regions of the brain or in particular cell types, and many lncRNAs are dynamically expressed during embryonic or postnatal neurogenesis. Less is known about the functions of these genes, if any, but they are increasingly implicated in diverse processes in health and disease. Here, we review the current knowledge about the roles and importance of lncRNAs in the central and peripheral nervous systems and discuss the specific niches within gene regulatory networks that might be preferentially occupied by lncRNAs.
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Affiliation(s)
- Hadas Hezroni
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rotem Ben Tov Perry
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
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Liu Y, Wang H. Peripheral nerve injury induced changes in the spinal cord and strategies to counteract/enhance the changes to promote nerve regeneration. Neural Regen Res 2020; 15:189-198. [PMID: 31552884 PMCID: PMC6905333 DOI: 10.4103/1673-5374.265540] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Peripheral nerve injury leads to morphological, molecular and gene expression changes in the spinal cord and dorsal root ganglia, some of which have positive impact on the survival of neurons and nerve regeneration, while the effect of others is the opposite. It is crucial to take prompt measures to capitalize on the positive effects of these reactions and counteract the negative impact after peripheral nerve injury at the level of spinal cord, especially for peripheral nerve injuries that are severe, located close to the cell body, involve long distance for axons to regrow and happen in immature individuals. Early nerve repair, exogenous supply of neurotrophic factors and Schwann cells can sustain the regeneration inductive environment and enhance the positive changes in neurons. Administration of neurotrophic factors, acetyl-L-carnitine, N-acetyl-cysteine, and N-methyl-D-aspartate receptor antagonist MK-801 can help counteract axotomy-induced neuronal loss and promote regeneration, which are all time-dependent. Sustaining and reactivation of Schwann cells after denervation provides another effective strategy. FK506 can be used to accelerate axonal regeneration of neurons, especially after chronic axotomy. Exploring the axotomy-induced changes after peripheral nerve injury and applying protective and promotional measures in the spinal cord which help to retain a positive functional status for neuron cell bodies will inevitably benefit regeneration of the peripheral nerve and improve functional outcomes.
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Affiliation(s)
- Yan Liu
- Department of Hand Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin Province, China; Department of Neurologic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Huan Wang
- Department of Neurologic Surgery, Mayo Clinic, Rochester, MN, USA
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Lin28 Signaling Supports Mammalian PNS and CNS Axon Regeneration. Cell Rep 2019; 24:2540-2552.e6. [PMID: 30184489 PMCID: PMC6173831 DOI: 10.1016/j.celrep.2018.07.105] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 04/05/2018] [Accepted: 07/30/2018] [Indexed: 02/07/2023] Open
Abstract
RNA-binding proteins Lin28a/b regulate cellular growth and tissue regeneration. Here, we investigated the role of Lin28 in the control of axon regeneration in postmitotic neurons. We find that Lin28a/b are both necessary and sufficient for supporting axon regeneration in mature sensory neurons through their regulatory partners, let-7 microRNAs (miRNAs). More importantly, overexpression of Lin28a in mature retinal ganglion cells (RGCs) produces robust and sustained optic nerve regeneration. Additionally, combined overexpression of Lin28a and downregulation of Pten in RGCs act additively to promote optic nerve regeneration, potentially by reducing the backward turning of regenerating RGC axons. Our findings not only reveal a vital role of Lin28 signaling in regulating mammalian axon regeneration but also identify a signaling pathway that can promote axon regeneration in the central nervous system (CNS). Axon regeneration in the mammalian CNS is a challenge. Wang et al. show that the Lin28/let-7 axis plays an important role in governing mammalian axon regeneration in the peripheral nervous system. More importantly, overexpression of Lin28a induces robust and sustained axon regeneration in the CNS.
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Telomerase Reverse Transcriptase and p53 Regulate Mammalian Peripheral Nervous System and CNS Axon Regeneration Downstream of c-Myc. J Neurosci 2019; 39:9107-9118. [PMID: 31597725 DOI: 10.1523/jneurosci.0419-19.2019] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 09/04/2019] [Accepted: 09/29/2019] [Indexed: 12/12/2022] Open
Abstract
Although several genes have been identified to promote axon regeneration in the CNS, our understanding of the molecular mechanisms by which mammalian axon regeneration is regulated is still limited and fragmented. Here by using female mouse sensory axon and optic nerve regeneration as model systems, we reveal an unexpected role of telomerase reverse transcriptase (TERT) in regulation of axon regeneration. We also provide evidence that TERT and p53 act downstream of c-Myc to control sensory axon regeneration. More importantly, overexpression of p53 in sensory neurons and retinal ganglion cells is sufficient to promote sensory axon and optic never regeneration, respectively. The study reveals a novel c-Myc-TERT-p53 signaling pathway, expanding horizons for novel approaches promoting CNS axon regeneration.SIGNIFICANCE STATEMENT Despite significant progress during the past decade, our understanding of the molecular mechanisms by which mammalian CNS axon regeneration is regulated is still fragmented. By using sensory axon and optic nerve regeneration as model systems, the study revealed an unexpected role of telomerase reverse transcriptase (TERT) in regulation of axon regeneration. The results also delineated a c-Myc-TERT-p53 pathway in controlling axon growth. Last, our results demonstrated that p53 alone was sufficient to promote sensory axon and optic nerve regeneration in vivo Collectively, the study not only revealed a new mechanisms underlying mammalian axon regeneration, but also expanded the pool of potential targets that can be manipulated to enhance CNS axon regeneration.
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Barros Ribeiro da Silva V, Porcionatto M, Toledo Ribas V. The Rise of Molecules Able To Regenerate the Central Nervous System. J Med Chem 2019; 63:490-511. [PMID: 31518122 DOI: 10.1021/acs.jmedchem.9b00863] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Injury to the adult central nervous system (CNS) usually leads to permanent deficits of cognitive, sensory, and/or motor functions. The failure of axonal regeneration in the damaged CNS limits functional recovery. The lack of information concerning the biological mechanism of axonal regeneration and its complexity has delayed the process of drug discovery for many years compared to other drug classes. Starting in the early 2000s, the ability of many molecules to stimulate axonal regrowth was evaluated through automated screening techniques; many hits and some new mechanisms involved in axonal regeneration were identified. In this Perspective, we discuss the rise of the CNS regenerative drugs, the main biological techniques used to test these drug candidates, some of the most important screens performed so far, and the main challenges following the identification of a drug that is able to induce axonal regeneration in vivo.
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Affiliation(s)
| | - Marimélia Porcionatto
- Universidade Federal de São Paulo , Escola Paulista de Medicina, Laboratório de Neurobiologia Molecular, Departmento de Bioquímica , Rua Pedro de Toledo, 669 - third floor, 04039-032 São Paulo , São Paolo , Brazil
| | - Vinicius Toledo Ribas
- Universidade Federal de Minas Gerais , Instituto de Ciências Biológicas, Departamento de Morfologia, Laboratório de Neurobiologia Av. Antônio Carlos, 6627, room O3-245 , - Campus Pampulha, 31270-901 , Belo Horizonte , Minas Gerais , Brazil
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39
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Miao Q, Hill MC, Chen F, Mo Q, Ku AT, Ramos C, Sock E, Lefebvre V, Nguyen H. SOX11 and SOX4 drive the reactivation of an embryonic gene program during murine wound repair. Nat Commun 2019; 10:4042. [PMID: 31492871 PMCID: PMC6731344 DOI: 10.1038/s41467-019-11880-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 08/08/2019] [Indexed: 01/08/2023] Open
Abstract
Tissue injury induces changes in cellular identity, but the underlying molecular mechanisms remain obscure. Here, we show that upon damage in a mouse model, epidermal cells at the wound edge convert to an embryonic-like state, altering particularly the cytoskeletal/extracellular matrix (ECM) components and differentiation program. We show that SOX11 and its closest relative SOX4 dictate embryonic epidermal state, regulating genes involved in epidermal development as well as cytoskeletal/ECM organization. Correspondingly, postnatal induction of SOX11 represses epidermal terminal differentiation while deficiency of Sox11 and Sox4 accelerates differentiation and dramatically impairs cell motility and re-epithelialization. Amongst the embryonic genes reactivated at the wound edge, we identify fascin actin-bundling protein 1 (FSCN1) as a critical direct target of SOX11 and SOX4 regulating cell migration. Our study identifies the reactivated embryonic gene program during wound repair and demonstrates that SOX11 and SOX4 play a central role in this process.
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Affiliation(s)
- Qi Miao
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, 1 Baylor Plaza, BCM 505, Houston, TX, 77030, USA.
- Center for Cell and Gene Therapy, Baylor College of Medicine, 1 Baylor Plaza, BCM 505, Houston, TX, 77030, USA.
| | - Matthew C Hill
- Program in Developmental Biology, Baylor College of Medicine, 1 Baylor Plaza, BCM 505, Houston, TX, 77030, USA
| | - Fengju Chen
- Dan L. Duncan Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, BCM 505, Houston, TX, 77030, USA
| | - Qianxing Mo
- Dan L. Duncan Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, BCM 505, Houston, TX, 77030, USA
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center, 12902 USF Magnolia Drive, Tampa, FL, 33612, USA
| | - Amy T Ku
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, 1 Baylor Plaza, BCM 505, Houston, TX, 77030, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, 1 Baylor Plaza, BCM 505, Houston, TX, 77030, USA
- Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, 1 Baylor Plaza, BCM 505, Houston, TX, 77030, USA
| | - Carlos Ramos
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, 1 Baylor Plaza, BCM 505, Houston, TX, 77030, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, 1 Baylor Plaza, BCM 505, Houston, TX, 77030, USA
| | - Elisabeth Sock
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Fahrstrasse 17, 91054, Erlangen, Germany
| | - Véronique Lefebvre
- Department of Surgery/Division of Orthopedic Surgery, Children's Hospital of Philadelphia, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Hoang Nguyen
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, 1 Baylor Plaza, BCM 505, Houston, TX, 77030, USA.
- Center for Cell and Gene Therapy, Baylor College of Medicine, 1 Baylor Plaza, BCM 505, Houston, TX, 77030, USA.
- Program in Developmental Biology, Baylor College of Medicine, 1 Baylor Plaza, BCM 505, Houston, TX, 77030, USA.
- Dan L. Duncan Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, BCM 505, Houston, TX, 77030, USA.
- Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, 1 Baylor Plaza, BCM 505, Houston, TX, 77030, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, 1 Baylor Plaza, BCM 505, Houston, TX, 77030, USA.
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Abstract
Permanent disabilities following CNS injuries result from the failure of injured axons to regenerate and rebuild functional connections with their original targets. By contrast, injury to peripheral nerves is followed by robust regeneration, which can lead to recovery of sensory and motor functions. This regenerative response requires the induction of widespread transcriptional and epigenetic changes in injured neurons. Considerable progress has been made in recent years in understanding how peripheral axon injury elicits these widespread changes through the coordinated actions of transcription factors, epigenetic modifiers and, to a lesser extent, microRNAs. Although many questions remain about the interplay between these mechanisms, these new findings provide important insights into the pivotal role of coordinated gene expression and chromatin remodelling in the neuronal response to injury.
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Affiliation(s)
- Marcus Mahar
- Department of Neuroscience, Hope Center for Neurological Disorders and Center of Regenerative Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Valeria Cavalli
- Department of Neuroscience, Hope Center for Neurological Disorders and Center of Regenerative Medicine, Washington University School of Medicine, St Louis, MO, USA.
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41
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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: 266] [Impact Index Per Article: 53.2] [Reference Citation Analysis] [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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42
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Yao C, Yu B. Role of Long Noncoding RNAs and Circular RNAs in Nerve Regeneration. Front Mol Neurosci 2019; 12:165. [PMID: 31316349 PMCID: PMC6611387 DOI: 10.3389/fnmol.2019.00165] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/14/2019] [Indexed: 12/19/2022] Open
Abstract
Nerve injuries may cause severe disability and affect the quality of life. It is of great importance to get a full understanding of the biological processes and molecular mechanisms underlying nerve injuries to find and target specific molecules for nerve regeneration. Numerous studies have shown that noncoding RNAs (ncRNAs) participate in diverse biological processes and diseases. Long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) are two major groups of ncRNAs, which attract growing attention. The altered expression patterns of lncRNAs and circRNAs following nerve injury suggest that these ncRNAs might be associated with nerve regeneration. This review will give a brief introduction of lncRNAs and circRNAs. We then summarize the current studies on lncRNAs and circRNAs following peripheral nerve injury and spinal cord injury (SCI). Typical lncRNAs and circRNAs are introduced to illustrate the diverse molecular mechanisms for nerve regeneration. In addition, we also discuss some issues to be addressed in future investigations on lncRNAs and circRNAs.
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Affiliation(s)
- Chun Yao
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Bin Yu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
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43
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Interleukin 1β inhibition contributes to the antinociceptive effects of voluntary exercise on ischemia/reperfusion-induced hypersensitivity. Pain 2019; 159:380-392. [PMID: 29112534 DOI: 10.1097/j.pain.0000000000001094] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Issues of peripheral circulation have been increasingly suggested as an underlying cause of musculoskeletal pain in many conditions, including sickle cell anemia and peripheral vascular disease. We have previously shown in our model of transient ischemia and reperfusion (I/R) injury of the forelimb that individual group III and IV muscle afferents display altered chemosensitivity and mechanical thresholds 1 day after injury. Functional alterations corresponded to increased evoked and spontaneous pain-related behaviors and decreased muscle strength and voluntary activity-all actions that echo clinical symptoms of ischemic myalgia. These behavioral and physiological changes appeared to originate in part from the action of increased interleukin 1β (IL1β) in the injured muscles at its upregulated IL1 receptor 1 within the dorsal root ganglion. Here, we describe that two days of voluntary wheel running prior to I/R blocks both injury-induced IL1β enhancement and the subsequent development of ischemic myalgia-like behaviors. Furthermore, the protective effects of 2 days prior exercise on the I/R-evoked increases in pain-related behaviors were also paralleled with systemic injection of the IL1 receptor antagonist during I/R. Interleukin 1 receptor antagonist treatment additionally prevented the I/R-induced changes in mechanical and chemical sensitivity of individual primary muscle afferents. Altogether, these data strengthen the evidence that transient I/R injury sensitizes group III and IV muscle afferents via increased IL1β in the muscles to stimulate ischemic myalgia development. Targeting IL1β may, therefore, be an effective treatment strategy for this insidious type of muscle pain.
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44
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Abstract
Traumatic brain and spinal cord injuries cause permanent disability. Although progress has been made in understanding the cellular and molecular mechanisms underlying the pathophysiological changes that affect both structure and function after injury to the brain or spinal cord, there are currently no cures for either condition. This may change with the development and application of multi-layer omics, new sophisticated bioinformatics tools, and cutting-edge imaging techniques. Already, these technical advances, when combined, are revealing an unprecedented number of novel cellular and molecular targets that could be manipulated alone or in combination to repair the injured central nervous system with precision. In this review, we highlight recent advances in applying these new technologies to the study of axon regeneration and rebuilding of injured neural circuitry. We then discuss the challenges ahead to translate results produced by these technologies into clinical application to help improve the lives of individuals who have a brain or spinal cord injury.
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Affiliation(s)
- Andrea Tedeschi
- Department of Neuroscience and Discovery Themes Initiative, College of Medicine, Ohio State University, Columbus, Ohio, 43210, USA
| | - Phillip G Popovich
- Center for Brain and Spinal Cord Repair, Institute for Behavioral Medicine Research, Ohio State University, Columbus, Ohio, 43210, USA
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45
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Harrison BJ, Park JW, Gomes C, Petruska JC, Sapio MR, Iadarola MJ, Chariker JH, Rouchka EC. Detection of Differentially Expressed Cleavage Site Intervals Within 3' Untranslated Regions Using CSI-UTR Reveals Regulated Interaction Motifs. Front Genet 2019; 10:182. [PMID: 30915105 PMCID: PMC6422928 DOI: 10.3389/fgene.2019.00182] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 02/19/2019] [Indexed: 01/08/2023] Open
Abstract
The length of untranslated regions at the 3' end of transcripts (3'UTRs) is regulated by alternate polyadenylation (APA). 3'UTRs contain regions that harbor binding motifs for regulatory molecules. However, the mechanisms that coordinate the 3'UTR length of specific groups of transcripts are not well-understood. We therefore developed a method, CSI-UTR, that models 3'UTR structure as tandem segments between functional alternative-polyadenylation sites (termed cleavage site intervals-CSIs). This approach facilitated (1) profiling of 3'UTR isoform expression changes and (2) statistical enrichment of putative regulatory motifs. CSI-UTR analysis is UTR-annotation independent and can interrogate legacy data generated from standard RNA-Seq libraries. CSI-UTR identified a set of CSIs in human and rodent transcriptomes. Analysis of RNA-Seq datasets from neural tissue identified differential expression events within 3'UTRs not detected by standard gene-based differential expression analyses. Further, in many instances 3'UTR and CDS from the same gene were regulated differently. This modulation of motifs for RNA-interacting molecules with potential condition-dependent and tissue-specific RNA binding partners near the polyA signal and CSI junction may play a mechanistic role in the specificity of alternative polyadenylation. Source code, CSI BED files and example datasets are available at: https://github.com/UofLBioinformatics/CSI-UTR.
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Affiliation(s)
- Benjamin J Harrison
- Department of Biomedical Sciences, Center for Excellence in the Neurosciences, College of Osteopathic Medicine, University of New England, Biddeford, ME, United States.,Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, United States.,Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, Louisville, KY, United States
| | - Juw Won Park
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, Louisville, KY, United States.,Department of Computer Engineering and Computer Science, Speed School of Engineering, University of Louisville, Louisville, KY, United States
| | - Cynthia Gomes
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, United States
| | - Jeffrey C Petruska
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, United States.,Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, KY, United States.,Department of Neurological Surgery, University of Louisville, Louisville, KY, United States
| | - Matthew R Sapio
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Michael J Iadarola
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Julia H Chariker
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, United States.,Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, Louisville, KY, United States
| | - Eric C Rouchka
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, Louisville, KY, United States.,Department of Computer Engineering and Computer Science, Speed School of Engineering, University of Louisville, Louisville, KY, United States
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46
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Ford ZK, Dourson AJ, Liu X, Lu P, Green KJ, Hudgins RC, Jankowski MP. Systemic growth hormone deficiency causes mechanical and thermal hypersensitivity during early postnatal development. IBRO Rep 2019; 6:111-121. [PMID: 30815617 PMCID: PMC6378845 DOI: 10.1016/j.ibror.2019.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 02/06/2019] [Indexed: 12/22/2022] Open
Abstract
Systemic GHD causes behavioral hypersensitivity at P7 and P14, but not P21. Primary afferent sensitization is observed in GHRHr KOs. Knockout of GHRHr changes DRG gene expression that is observed throughout development.
Injury during early postnatal life causes acute alterations in afferent function and DRG gene expression, which in addition to producing short-term sensitivity has the potential to influence nociceptive responses in adulthood. We recently discovered that growth hormone (GH) is a key regulator of afferent sensitization and pain-related behaviors during developmental inflammation of the skin. Peripheral injury caused a significant reduction in cutaneous GH levels, which corresponded with the observed hypersensitivity. However, it has yet to be determined whether GH deficiency (GHD) is sufficient to drive peripheral sensitization in uninjured animals. Here, we found that systemic GHD, induced by knockout of the GH release hormone receptor (GHRHr), was able to induce behavioral and afferent hypersensitivity to peripheral stimuli specifically during early developmental stages. GHD also produced an upregulation of many receptors and channels linked to nociceptive processing in the DRGs at these early postnatal ages (P7 and P14). Surprisingly, P21 GHRHr knockouts also displayed significant alterations in DRG gene expression even though behavioral and afferent hypersensitivity resolved. These data support previous findings that GH is a key modulator of neonatal hypersensitivity. Results may provide insight into whether GH treatment may be a therapeutic strategy for pediatric pain.
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Affiliation(s)
- Zachary K. Ford
- Department of Anesthesia, Division of Pain Management, Cincinnati Children’s Hospital Medical Center, United States
| | - Adam J. Dourson
- Department of Anesthesia, Division of Pain Management, Cincinnati Children’s Hospital Medical Center, United States
| | - Xiaohua Liu
- Department of Anesthesia, Division of Pain Management, Cincinnati Children’s Hospital Medical Center, United States
| | - Peilin Lu
- Department of Anesthesia, Division of Pain Management, Cincinnati Children’s Hospital Medical Center, United States
| | - Kathryn J. Green
- Department of Anesthesia, Division of Pain Management, Cincinnati Children’s Hospital Medical Center, United States
| | - Renita C. Hudgins
- Department of Anesthesia, Division of Pain Management, Cincinnati Children’s Hospital Medical Center, United States
| | - Michael P. Jankowski
- Department of Anesthesia, Division of Pain Management, Cincinnati Children’s Hospital Medical Center, United States
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati OH 45229, United States
- Corresponding author at: Department of Anesthesia, Division of Pain Management, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Ave MLC 6016, Cincinnati, OH 45229, United States.
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Li Y, Struebing FL, Wang J, King R, Geisert EE. Different Effect of Sox11 in Retinal Ganglion Cells Survival and Axon Regeneration. Front Genet 2018; 9:633. [PMID: 30619460 PMCID: PMC6305287 DOI: 10.3389/fgene.2018.00633] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/27/2018] [Indexed: 12/20/2022] Open
Abstract
Purpose: The present study examines the role of Sox11 in the initial response of retinal ganglion cells (RGCs) to axon damage and in optic nerve regeneration in mouse. Methods: Markers of retinal injury were identified using the normal retina database and optic nerve crush (ONC) database on GeneNetwork2 (www.genenetwork.org). One gene, Sox11, was highly upregulated following ONC. We examined the role of this transcription factor, Sox11, following ONC and optic nerve regeneration in mice. In situ hybridization was performed using the Affymetrix 2-plex Quantigene View RNA In Situ Hybridization Tissue Assay System. Sox11 was partially knocked out by intravitreal injection of AAV2-CMV-Cre-GFP in Sox11 f/f mice. Optic nerve regeneration model used Pten knockdown. Mice were perfused and the retinas and optic nerves were dissected and examined for RGC survival and axon growth. Results: Sox11 was dramatically upregulated in the retina following ONC injury. The level of Sox11 message increased by approximately eightfold 2 days after ONC. In situ hybridization demonstrated low-level Sox11 message in RGCs and cells in the inner nuclear layer in the normal retina as well as a profound increase in Sox11 message within the ganglion cells following ONC. In Sox11 f/f retinas, partially knocking out Sox11 significantly increased RGC survival after ONC as compared to the AAV2-CMV-GFP control group; however, it had little effect on the ability of axon regeneration. Combinatorial downregulation of both Sox11 and Pten resulted in a significant increase in RGC survival as compared to Pten knockdown only. When Pten was knocked down there was a remarkable increase in the number and the length of regenerating axons. Partially knocking out Sox11 in combination with Pten deletion resulted in a fewer regenerating axons. Conclusion: Taken together, these data demonstrate that Sox11 is involved in the initial response of the retina to injury, playing a role in the early attempts of axon regeneration and neuronal survival. Downregulation of Sox11 aids in RGC survival following injury of optic nerve axons, while a partial knockout of Sox11 negates the axon regeneration stimulated by Pten knockdown.
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Affiliation(s)
- Ying Li
- Department of Ophthalmology, Emory University, Atlanta, GA, United States
| | - Felix L Struebing
- Department of Ophthalmology, Emory University, Atlanta, GA, United States.,Center for Neuropathology and Prion Research, Ludwig Maximilian University of Munich, Munich, Germany.,Department for Translational Brain Research, German Center for Neurodegenerative Diseases, Munich, Germany
| | - Jiaxing Wang
- Department of Ophthalmology, Emory University, Atlanta, GA, United States
| | - Rebecca King
- Department of Ophthalmology, Emory University, Atlanta, GA, United States
| | - Eldon E Geisert
- Department of Ophthalmology, Emory University, Atlanta, GA, United States
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48
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Regulation of Neuroregeneration by Long Noncoding RNAs. Mol Cell 2018; 72:553-567.e5. [PMID: 30401432 DOI: 10.1016/j.molcel.2018.09.021] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 07/27/2018] [Accepted: 09/14/2018] [Indexed: 12/24/2022]
Abstract
In mammals, neurons in the peripheral nervous system (PNS) have regenerative capacity following injury, but it is generally absent in the CNS. This difference is attributed, at least in part, to the intrinsic ability of PNS neurons to activate a unique regenerative transcriptional program following injury. Here, we profiled gene expression following sciatic nerve crush in mice and identified long noncoding RNAs (lncRNAs) that act in the regenerating neurons and which are typically not expressed in other contexts. We show that two of these lncRNAs regulate the extent of neuronal outgrowth. We then focus on one of these, Silc1, and show that it regulates neuroregeneration in cultured cells and in vivo, through cis-acting activation of the transcription factor Sox11.
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Curcio M, Bradke F. Axon Regeneration in the Central Nervous System: Facing the Challenges from the Inside. Annu Rev Cell Dev Biol 2018; 34:495-521. [DOI: 10.1146/annurev-cellbio-100617-062508] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
After an injury in the adult mammalian central nervous system (CNS), lesioned axons fail to regenerate. This failure to regenerate contrasts with axons’ remarkable potential to grow during embryonic development and after an injury in the peripheral nervous system (PNS). Several intracellular mechanisms—including cytoskeletal dynamics, axonal transport and trafficking, signaling and transcription of regenerative programs, and epigenetic modifications—control axon regeneration. In this review, we describe how manipulation of intrinsic mechanisms elicits a regenerative response in different organisms and how strategies are implemented to form the basis of a future regenerative treatment after CNS injury.
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Affiliation(s)
- Michele Curcio
- Laboratory for Axon Growth and Regeneration, German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany;,
| | - Frank Bradke
- Laboratory for Axon Growth and Regeneration, German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany;,
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Lu P, Hudgins RC, Liu X, Ford ZK, Hofmann MC, Queme LF, Jankowski MP. Upregulation of P2Y1 in neonatal nociceptors regulates heat and mechanical sensitization during cutaneous inflammation. Mol Pain 2018; 13:1744806917730255. [PMID: 28845731 PMCID: PMC5590703 DOI: 10.1177/1744806917730255] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The upregulation of various channels and receptors classically linked to sensory transduction from the periphery tightly correspond with changes in the responsiveness of specific subpopulations of primary afferents to mechanical and heat stimulation of the skin at different ages. Previous reports in adults have suggested that the purinergic adenosine diphosphate receptor, P2Y1 can specifically regulate sensory neuron responsiveness to heat stimuli in addition to neurochemical alterations in primary afferents during cutaneous inflammation. To determine if the upregulation of P2Y1 found in the dorsal root ganglia of neonatal mice with cutaneous inflammation initiated at postnatal day 7 (P7) was responsible for the specific alteration in heat sensitivity found in faster conducting (“A”-fiber) nociceptors, we assessed the response properties of cutaneous afferents using an ex vivo hairy hindpaw skin-saphenous nerve-dorsal root ganglion-spinal cord preparation in conjunction with nerve-targeted knockdown of P2Y1. We found that P2Y1 knockdown during neonatal cutaneous inflammation was sufficient to reduce the sensitization of “A”-fiber nociceptors to heat stimuli. Surprisingly, we also found that nerve-specific downregulation of P2Y1 could reduce the observed sensitization of these afferent subtypes to mechanical deformation of the skin. Immunocytochemical analysis of dorsal root ganglia showed that P2Y1 may mediate its effects through modulation of the injury-induced increase of transient receptor potential vanilloid type 1 receptor. This suggests that the upregulation of P2Y1 in cutaneous nociceptors during early life peripheral inflammation can regulate the sensitization of myelinated nociceptors to both mechanical and heat stimuli possibly through modulation of transient receptor potential vanilloid type 1 expression.
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Affiliation(s)
- Peilin Lu
- Department of Anesthesia, Division of Pain Management, Cincinnati Children's Hospital Medical Center
| | - Renita C Hudgins
- Department of Anesthesia, Division of Pain Management, Cincinnati Children's Hospital Medical Center
| | - Xiaohua Liu
- Department of Anesthesia, Division of Pain Management, Cincinnati Children's Hospital Medical Center
| | - Zachary K Ford
- Department of Anesthesia, Division of Pain Management, Cincinnati Children's Hospital Medical Center
| | - Megan C Hofmann
- Department of Anesthesia, Division of Pain Management, Cincinnati Children's Hospital Medical Center
| | - Luis F Queme
- Department of Anesthesia, Division of Pain Management, Cincinnati Children's Hospital Medical Center
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