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Wang S, Qian W, Chen S, Xian S, Jin M, Liu Y, Zhang H, Qin H, Zhang X, Zhu J, Yue X, Shi C, Yan P, Huang R, Huang Z. Bibliometric analysis of research on gene expression in spinal cord injury. Front Mol Neurosci 2022; 15:1023692. [PMID: 36385766 PMCID: PMC9661966 DOI: 10.3389/fnmol.2022.1023692] [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] [Received: 08/20/2022] [Accepted: 10/10/2022] [Indexed: 11/29/2022] Open
Abstract
Background Spinal cord injury (SCI) is a severe disease with motor and sensory function being destroyed, which leads to a poor prognosis and a serious financial burden. It is urgent to figure out the molecular and pathological mechanisms of SCI to develop feasible therapeutic strategies. This article aims to review documents focused on gene expression in SCI and summarize research hotspots and the development process in this field. Methods Publications of SCI-related studies from 2000 to 2022 were retrieved from the Web of Science Core Collection database. Biblioshiny was used to evaluate the research performance, core authors, journals and contributed countries, together with trend topics, hotspots in the field, and keyword co-occurrence analysis. Visualized images were obtained to help comprehension. Results Among 351 documents, it was found that the number of annual publications increased in general. The most productive country was China, followed by the United States with the highest influence and the most international cooperation. Plos One was the journal of the maximum publications, while Journal of Neuroscience was the most influential one. According to keyword co-occurrence and trend topics analysis, these articles mainly focused on molecular and pathological mechanisms as well as novel therapies for SCI. Neuropathic pain, axonal regeneration and messenger RNA are significant and promising research areas. Conclusion As the first bibliometric study focused on gene expression in SCI, we demonstrated the evolution of the field and provided future research directions like mechanisms and treatments of SCI with great innovativeness and clinical value. Further studies are recommended to develop more viable therapeutic methods for SCI.
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Affiliation(s)
- Siqiao Wang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Division of Spine, Department of Orthopedics, Tongji Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
- Tongji University School of Medicine, Shanghai, China
| | - Weijin Qian
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shaofeng Chen
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Shuyuan Xian
- Tongji University School of Medicine, Shanghai, China
| | - Minghao Jin
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yifan Liu
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hao Zhang
- Department of Orthopedics, Naval Medical Center of PLA, Second Military Medical University Shanghai, Shanghai, China
| | - Hengwei Qin
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinkun Zhang
- Tongji University School of Medicine, Shanghai, China
| | - Jiwen Zhu
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xi Yue
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chaofeng Shi
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Penghui Yan
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Zongqiang Huang, ; Runzhi Huang, ; Penghui Yan,
| | - Runzhi Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, China
- Research Unit of Key Techniques for Treatment of Burns and Combined Burns and Trauma Injury, Chinese Academy of Medical Sciences, Shanghai, China
- *Correspondence: Zongqiang Huang, ; Runzhi Huang, ; Penghui Yan,
| | - Zongqiang Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Zongqiang Huang, ; Runzhi Huang, ; Penghui Yan,
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Pathophysiology, Classification and Comorbidities after Traumatic Spinal Cord Injury. J Pers Med 2022; 12:jpm12071126. [PMID: 35887623 PMCID: PMC9323191 DOI: 10.3390/jpm12071126] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 12/25/2022] Open
Abstract
The spinal cord is a conduit within the central nervous system (CNS) that provides ongoing communication between the brain and the rest of the body, conveying complex sensory and motor information necessary for safety, movement, reflexes, and optimization of autonomic function. After a spinal cord injury (SCI), supraspinal influences on the spinal segmental control system and autonomic nervous system (ANS) are disrupted, leading to spastic paralysis, pain and dysesthesia, sympathetic blunting and parasympathetic dominance resulting in cardiac dysrhythmias, systemic hypotension, bronchoconstriction, copious respiratory secretions and uncontrolled bowel, bladder, and sexual dysfunction. This article outlines the pathophysiology of traumatic SCI, current and emerging methods of classification, and its influence on sensory/motor function, and introduces the probable comorbidities associated with SCI that will be discussed in more detail in the accompanying manuscripts of this special issue.
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Niu SP, Zhang YJ, Han N, Yin XF, Zhang DY, Kou YH. Identification of four differentially expressed genes associated with acute and chronic spinal cord injury based on bioinformatics data. Neural Regen Res 2021; 16:865-870. [PMID: 33229721 PMCID: PMC8178775 DOI: 10.4103/1673-5374.297087] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Complex pathological changes occur during the development of spinal cord injury (SCI), and determining the underlying molecular events that occur during SCI is necessary for the development of promising molecular targets and therapeutic strategies. This study was designed to explore differentially expressed genes (DEGs) associated with the acute and chronic stages of SCI using bioinformatics analysis. Gene expression profiles (GSE45006, GSE93249, and GSE45550) were downloaded from the Gene Expression Omnibus database. SCI-associated DEGs from rat samples were identified, and Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed. In addition, a protein-protein interaction network was constructed. Approximately 66 DEGs were identified in GSE45550 between 3–14 days after SCI, whereas 2418 DEGs were identified in GSE45006 1–56 days after SCI. Moreover, 1263, 195, and 75 overlapping DEGs were identified between these two expression profiles, 3, 7/8, and 14 days after SCI, respectively. Additionally, 16 overlapping DEGs were obtained in GSE45006 1–14 days after SCI, including Pank1, Hn1, Tmem150c, Rgd1309676, Lpl, Mdh1, Nnt, Loc100912219, Large1, Baiap2, Slc24a2, Fundc2, Mrps14, Slc16a7, Obfc1, and Alpk3. Importantly, 3882 overlapping DEGs were identified in GSE93249 1–6 months after SCI, including 3316 protein-coding genes and 567 long non-coding RNA genes. A comparative analysis between GSE93249 and GSE45006 resulted in the enrichment of 1135 overlapping DEGs. The significant functions of these 1135 genes were correlated with the response to the immune effector process, the innate immune response, and cytokine production. Moreover, the biological processes and KEGG pathways of the overlapping DEGs were significantly enriched in immune system-related pathways, osteoclast differentiation, the nuclear factor-κB signaling pathway, and the chemokine signaling pathway. Finally, an analysis of the overlapping DEGs associated with both acute and chronic SCI, assessed using the expression profiles GSE93249 and GSE45006, identified four overlapping DEGs: Slc16a7, Alpk3, Lpl and Nnt. These findings may be useful for revealing the biological processes associated with SCI and the development of targeted intervention strategies.
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Affiliation(s)
- Su-Ping Niu
- Key Laboratory of Trauma and Neural Regeneration (Peking University), Ministry of Education; Office of Academic Research, Peking University People's Hospital, Beijing, China
| | - Ya-Jun Zhang
- Key Laboratory of Trauma and Neural Regeneration (Peking University), Ministry of Education; Trauma Medicine Center, Peking University People's Hospital, Beijing, China
| | - Na Han
- Key Laboratory of Trauma and Neural Regeneration (Peking University), Ministry of Education; Office of Academic Research, Peking University People's Hospital, Beijing, China
| | - Xiao-Feng Yin
- Key Laboratory of Trauma and Neural Regeneration (Peking University), Ministry of Education; Department of Trauma and Orthopedics, Peking University People's Hospital, Beijing, China
| | - Dian-Ying Zhang
- Key Laboratory of Trauma and Neural Regeneration (Peking University), Ministry of Education; Department of Trauma and Orthopedics, Peking University People's Hospital, Beijing, China
| | - Yu-Hui Kou
- Key Laboratory of Trauma and Neural Regeneration (Peking University), Ministry of Education; Department of Trauma and Orthopedics, Peking University People's Hospital, Beijing, China
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Chen J, Wu Y, Duan FX, Wang SN, Guo XY, Ding SQ, Zhou JH, Hu JG, Lü HZ. Effect of M2 macrophage adoptive transfer on transcriptome profile of injured spinal cords in rats. Exp Biol Med (Maywood) 2019; 244:880-892. [PMID: 31159561 DOI: 10.1177/1535370219854668] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The previous studies showed that alternatively activated anti-inflammatory macrophage (M2) adoptive immunity can improve the proportion of local M2 cells and play the neuroprotective effect after spinal cord injury (SCI). Its molecular mechanism is not yet very clear. Therefore, this study aims to analyze the effect of the M2 adoptive transfer on the local expression of gene transcription. Sprague-Dawley (SD) rats were used for culture of macrophages and establishment of SCI models. After SCI, the polarized M2 macrophages were transferred to the injured rats by tail vein injection. Seven days after operation, the differentially expressed genes (DEGs) in the spinal cords were analyzed by RNA-sequencing (RNA-Seq). Then, the functional enrichment analysis and pathways were performed by using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), respectively. RNA-Seq showed that M2 adoptive immunity can down-regulate many well-studied gene expressions associated with signaling pathways of inflammatory, such as antigen processing and presentation, phagosome, cell adhesion molecules, natural killer cell-mediated cytotoxicity, endocytosis, proteasome, and Toll-like receptor signaling pathway. These may explain the mechanism of our previous adoptive immunization of M2 cells to provide neuroprotection for SCI. In addition, a novel pathway, retinoic acid-inducible gene-1 (RIG-I)-like receptor signaling pathway was found to be involved in the pathological process of SCI and the response to M2 adoptive immunity as well. This will provide a new explanation for the pathological mechanism of SCI and a new theoretical and experimental basis for its clinical treatment. The raw Illumina data are available at http://www.ncbi.nlm.nih.gov/sra (accession number PRJNA517238). Impact statement This research aimed to analyze the effect of M2 macrophage adoptive transfer on the local expression of gene transcription after SCI by RNA-Seq. The results showed that M2 adoptive immunity can down-regulate many well-studied gene expressions associated with signaling pathways of inflammatory. These may explain the mechanism of our previous adoptive immunization of M2 cells to provide neuroprotection for SCI. In addition, a novel pathway, RIG-I-like receptor signaling pathway was also found to involve in the pathological process of SCI and the response to M2 adoptive immunity. This will provide a new explanation for the pathological mechanism of SCI and a new theoretical and experimental basis for its clinical treatment.
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Affiliation(s)
- Jing Chen
- 1 Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China.,2 Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China.,3 Department of Immunology, Bengbu Medical College, Anhui 233030, PR China
| | - Yan Wu
- 1 Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China.,2 Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China.,3 Department of Immunology, Bengbu Medical College, Anhui 233030, PR China
| | - Fei-Xiang Duan
- 1 Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China.,2 Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China
| | - Sai-Nan Wang
- 1 Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China.,2 Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China.,3 Department of Immunology, Bengbu Medical College, Anhui 233030, PR China
| | - Xue-Yan Guo
- 1 Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China.,2 Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China
| | - Shu-Qin Ding
- 1 Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China.,2 Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China
| | - Ji-Hong Zhou
- 3 Department of Immunology, Bengbu Medical College, Anhui 233030, PR China
| | - Jian-Guo Hu
- 1 Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China.,2 Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China
| | - He-Zuo Lü
- 1 Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China.,2 Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China.,3 Department of Immunology, Bengbu Medical College, Anhui 233030, PR China
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RNA Sequencing of Peripheral Blood Revealed that the Neurotropic TRK Receptor Signaling Pathway Shows Apparent Correlation in Recovery Following Spinal Cord Injury at Small Cohort. J Mol Neurosci 2019; 68:221-233. [PMID: 30993646 DOI: 10.1007/s12031-019-01273-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/29/2019] [Indexed: 12/14/2022]
Abstract
Spinal cord injury (SCI) can be lethal; however, the precise mechanisms underlying healing are unclear, limiting the development of effective therapies. In this study, the molecular mechanisms involved in SCI were investigated. Clinical peripheral blood samples from normal individuals and patients with incomplete SCI (ISCI) and complete SCI (CSCI) were analyzed by RNA-Seq. The expression levels of EPHA4, CDK16, BAD, MAP2 Normal 2, EGR, and RHOB differed significantly between the SCI group and normal individuals, and these results were verified by q-PCR. A gene ontology (GO) enrichment analysis showed that differentially expressed genes were mostly enriched for the neurotrophin TRK receptor signaling pathway. We verified the expression of neurotrophic factors and found that they were all expressed most highly in the SCI group. The results of this study demonstrate that neurotrophic factors are highly expressed after SCI and the neurotrophin TRK receptor signaling pathway may be involved in the initiation of nerve system regeneration.
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Tang Y, Liu HL, Min LX, Yuan HS, Guo L, Han PB, Lu YX, Zhong JF, Wang DL. Serum and cerebrospinal fluid tau protein level as biomarkers for evaluating acute spinal cord injury severity and motor function outcome. Neural Regen Res 2019; 14:896-902. [PMID: 30688276 PMCID: PMC6375043 DOI: 10.4103/1673-5374.249238] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Tau protein, a microtubule-associated protein, has a high specific expression in neurons and axons. Because traumatic spinal cord injury mainly affects neurons and axons, we speculated that tau protein may be a promising biomarker to reflect the degree of spinal cord injury and prognosis of motor function. In this study, 160 female Sprague-Dawley rats were randomly divided into a sham group, and mild, moderate, and severe spinal cord injury groups. A laminectomy was performed at the T8 level to expose the spinal cord in all groups. A contusion lesion was made with the NYU-MASCIS impactor by dropping a 10 g rod from heights of 12.5 mm (mild), 25 mm (moderate) and 50 mm (severe) upon the exposed dorsal surface of the spinal cord. Tau protein levels were measured in serum and cerebrospinal fluid samples at 1, 6, 12, 24 hours, 3, 7, 14 and 28 days after operation. Locomotor function of all rats was assessed using the Basso, Beattie and Bresnahan locomotor rating scale. Tau protein concentration in the three spinal cord injury groups (both in serum and cerebrospinal fluid) rapidly increased and peaked at 12 hours after spinal cord injury. Statistically significant positive linear correlations were found between tau protein level and spinal cord injury severity in the three spinal cord injury groups, and between the tau protein level and Basso, Beattie, and Bresnahan locomotor rating scale scores. The tau protein level at 12 hours in the three spinal cord injury groups was negatively correlated with Basso, Beattie, and Bresnahan locomotor rating scale scores at 28 days (serum: r = −0.94; cerebrospinal fluid: r = −0.95). Our data suggest that tau protein levels in serum and cerebrospinal fluid might be a promising biomarker for predicting the severity and functional outcome of traumatic spinal cord injury.
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Affiliation(s)
- Ying Tang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education (Chongqing University), Chongqing University Cancer Hospital, Chongqing, China
| | - Hong-Liang Liu
- Department of Rehabilitation, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Ling-Xia Min
- Department of Rehabilitation, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Hao-Shi Yuan
- Department of Spine Surgery, Second Affiliated Hospital of Xi'an Medical University, Xi'an, Shanxi Province, China
| | - Lei Guo
- Department of Orthopedics, Chinese PLA Beijing Army General Hospital, Beijing, China
| | - Peng-Bo Han
- Department of Spine Surgery, Second Affiliated Hospital of Xi'an Medical University, Xi'an, Shanxi Province, China
| | - Yu-Xin Lu
- Department of Spine Surgery, Second Affiliated Hospital of Xi'an Medical University, Xi'an, Shanxi Province, China
| | - Jian-Feng Zhong
- Department of Spine Surgery, Second Affiliated Hospital of Xi'an Medical University, Xi'an, Shanxi Province, China
| | - Dong-Lin Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education (Chongqing University), Chongqing University Cancer Hospital, Chongqing, China
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Zhao SJ, Zhou W, Chen J, Luo YJ, Yin GY. Bioinformatics analysis of the molecular mechanisms underlying traumatic spinal cord injury. Mol Med Rep 2018; 17:8484-8492. [PMID: 29693160 DOI: 10.3892/mmr.2018.8918] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 02/07/2018] [Indexed: 11/06/2022] Open
Abstract
Spinal cord injury (SCI) is a cause of disability. The present study aimed to investigate the molecular mechanisms involved in traumatic SCI. Transcriptome data under accession no. GSE5296, including 96 chips, were downloaded from the Gene Expression Omnibus database. The raw data were normalized and differentially expressed genes (DEGs) were identified. Furthermore, Kyoto Encyclopedia of Genes and Genomes pathway and Gene Ontology enrichment analysis of up‑ and downregulated DEGs was performed. Additionally, a protein‑protein interaction network was constructed and the expression patterns of different genes were determined. Compared with sham samples, there were 374, 707, 1,322, 1,475, 1,724 and 1,342 DEGs identified at 0.5, 4, 24 and 72 h, and 7 and 28 days post‑injury, respectively. At 24 and 72 h, and 7 days following injury, the upregulated DEGs were markedly enriched in 'inflammatory response' and 'immune process'. Downregulated DEGs were predominantly enriched in neuronal function‑associated pathways and 'steroid biosynthesis' process. Protein‑protein interaction network analysis demonstrated similar results. Trend charts further demonstrated that the inflammatory and neuronal functions were altered in a temporal and site‑specific manner. The present study provided an insight into the molecular mechanisms underlying traumatic SCI, which may benefit future SCI research and aid in therapy development.
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Affiliation(s)
- Shu-Jie Zhao
- Department of Orthopedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Wei Zhou
- Department of Orthopedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Jian Chen
- Department of Orthopedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Yong-Jun Luo
- Department of Orthopedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Guo-Yong Yin
- Department of Orthopedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
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Bhore N, Wang BJ, Chen YW, Liao YF. Critical Roles of Dual-Specificity Phosphatases in Neuronal Proteostasis and Neurological Diseases. Int J Mol Sci 2017; 18:ijms18091963. [PMID: 28902166 PMCID: PMC5618612 DOI: 10.3390/ijms18091963] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/01/2017] [Accepted: 09/07/2017] [Indexed: 12/31/2022] Open
Abstract
Protein homeostasis or proteostasis is a fundamental cellular property that encompasses the dynamic balancing of processes in the proteostasis network (PN). Such processes include protein synthesis, folding, and degradation in both non-stressed and stressful conditions. The role of the PN in neurodegenerative disease is well-documented, where it is known to respond to changes in protein folding states or toxic gain-of-function protein aggregation. Dual-specificity phosphatases have recently emerged as important participants in maintaining balance within the PN, acting through modulation of cellular signaling pathways that are involved in neurodegeneration. In this review, we will summarize recent findings describing the roles of dual-specificity phosphatases in neurodegeneration and offer perspectives on future therapeutic directions.
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Affiliation(s)
- Noopur Bhore
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Yang-Ming University and Academia Sinica, Taipei 11529, Taiwan.
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan.
| | - Bo-Jeng Wang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan.
| | - Yun-Wen Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan.
| | - Yung-Feng Liao
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Yang-Ming University and Academia Sinica, Taipei 11529, Taiwan.
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan.
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9
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Shi LL, Zhang N, Xie XM, Chen YJ, Wang R, Shen L, Zhou JS, Hu JG, Lü HZ. Transcriptome profile of rat genes in injured spinal cord at different stages by RNA-sequencing. BMC Genomics 2017; 18:173. [PMID: 28201982 PMCID: PMC5312572 DOI: 10.1186/s12864-017-3532-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 02/01/2017] [Indexed: 12/15/2022] Open
Abstract
Background Spinal cord injury (SCI) results in fatal damage and currently has no effective treatment. The pathological mechanisms of SCI remain unclear. In this study, genome-wide transcriptional profiling of spinal cord samples from injured rats at different time points after SCI was performed by RNA-Sequencing (RNA-Seq). The transcriptomes were systematically characterized to identify the critical genes and pathways that are involved in SCI pathology. Results RNA-Seq results were obtained from total RNA harvested from the spinal cords of sham control rats and rats in the acute, subacute, and chronic phases of SCI (1 day, 6 days and 28 days after injury, respectively; n = 3 in every group). Compared with the sham-control group, the number of differentially expressed genes was 1797 in the acute phase (1223 upregulated and 574 downregulated), 6590 in the subacute phase (3460 upregulated and 3130 downregulated), and 3499 in the chronic phase (1866 upregulated and 1633 downregulated), with an adjusted P-value <0.05 by DESeq. Gene ontology (GO) enrichment analysis showed that differentially expressed genes were most enriched in immune response, MHC protein complex, antigen processing and presentation, translation-related genes, structural constituent of ribosome, ion gated channel activity, small GTPase mediated signal transduction and cytokine and/or chemokine activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the most enriched pathways included ribosome, antigen processing and presentation, retrograde endocannabinoid signaling, axon guidance, dopaminergic synapses, glutamatergic synapses, GABAergic synapses, TNF, HIF-1, Toll-like receptor, NF-kappa B, NOD-like receptor, cAMP, calcium, oxytocin, Rap1, B cell receptor and chemokine signaling pathway. Conclusions This study has not only characterized changes in global gene expression through various stages of SCI progression in rats, but has also systematically identified the critical genes and signaling pathways in SCI pathology. These results will expand our understanding of the complex molecular mechanisms involved in SCI and provide a foundation for future studies of spinal cord tissue damage and repair. The sequence data from this study have been deposited into Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra; accession number PRJNA318311). Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3532-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ling-Ling Shi
- Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui, 233004, People's Republic of China.,Department of Immunology, Bengbu Medical College, Anhui, 233030, People's Republic of China
| | - Nan Zhang
- Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, 287 Chang Huai Road, Anhui, 233004, People's Republic of China
| | - Xiu-Mei Xie
- Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui, 233004, People's Republic of China.,Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, 287 Chang Huai Road, Anhui, 233004, People's Republic of China
| | - Yue-Juan Chen
- Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui, 233004, People's Republic of China.,Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, 287 Chang Huai Road, Anhui, 233004, People's Republic of China
| | - Rui Wang
- Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, 287 Chang Huai Road, Anhui, 233004, People's Republic of China
| | - Lin Shen
- Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui, 233004, People's Republic of China.,Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, 287 Chang Huai Road, Anhui, 233004, People's Republic of China
| | - Jian-Sheng Zhou
- Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, 287 Chang Huai Road, Anhui, 233004, People's Republic of China
| | - Jian-Guo Hu
- Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui, 233004, People's Republic of China. .,Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, 287 Chang Huai Road, Anhui, 233004, People's Republic of China.
| | - He-Zuo Lü
- Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui, 233004, People's Republic of China. .,Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, 287 Chang Huai Road, Anhui, 233004, People's Republic of China. .,Department of Immunology, Bengbu Medical College, Anhui, 233030, People's Republic of China.
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10
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Pharmacological inhibition of spinal cord injury-stimulated ribosomal biogenesis does not affect locomotor outcome. Neurosci Lett 2017; 642:153-157. [PMID: 28188847 DOI: 10.1016/j.neulet.2017.02.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 01/20/2017] [Accepted: 02/06/2017] [Indexed: 12/20/2022]
Abstract
After unresolved endoplasmic reticulum stress, recovery of protein synthesis including increased expression of ribosomal components and translation factors may induce cell death. Using a mouse model of moderate contusive spinal cord injury (SCI) at the T9 level, upregulation of ribosomal biogenesis was observed in the injury epicenter at 24h after trauma. Such upregulation coincided with endoplasmic reticulum stress response as previously reported in this model. It was also accompanied by changes in expression of many other genes associated with translational regulation. Systemic treatment with a pharmacological inhibitor of RNA-Polymerase-1, BMH-21 reduced rRNA transcription in the spinal cord. Moreover, in the injury epicenter, treatment with BMH-21 increased expression of oligodendrocyte-specific transcripts including Mbp and Cldn11 at 3days post injury. Although such findings may suggest at least transient reduction of oligodendrocyte death, locomotor outcome was mostly unaffected except slightly accelerated recovery of hindlimb function at week 2 post-injury. Therefore, at least in mice, RNA-Polymerase-1 does not appear to be a robust target for therapies to protect spinal cord tissue after contusion. However, these findings raise an interesting possibility that altered rate of ribosomal biogenesis contributes to the apparent translational reprogramming after contusive SCI. Such a reprogramming could be a major regulator of SCI-induced gene expression.
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Koehn LM, Noor NM, Dong Q, Er SY, Rash LD, King GF, Dziegielewska KM, Saunders NR, Habgood MD. Selective inhibition of ASIC1a confers functional and morphological neuroprotection following traumatic spinal cord injury. F1000Res 2016; 5:1822. [PMID: 28105306 PMCID: PMC5200949 DOI: 10.12688/f1000research.9094.2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/29/2016] [Indexed: 12/31/2022] Open
Abstract
Tissue loss after spinal trauma is biphasic, with initial mechanical/haemorrhagic damage at the time of impact being followed by gradual secondary expansion into adjacent, previously unaffected tissue. Limiting the extent of this secondary expansion of tissue damage has the potential to preserve greater residual spinal cord function in patients. The acute tissue hypoxia resulting from spinal cord injury (SCI) activates acid-sensing ion channel 1a (ASIC1a). We surmised that antagonism of this channel should provide neuroprotection and functional preservation after SCI. We show that systemic administration of the spider-venom peptide PcTx1, a selective inhibitor of ASIC1a, improves locomotor function in adult Sprague Dawley rats after thoracic SCI. The degree of functional improvement correlated with the degree of tissue preservation in descending white matter tracts involved in hind limb locomotor function. Transcriptomic analysis suggests that PcTx1-induced preservation of spinal cord tissue does not result from a reduction in apoptosis, with no evidence of down-regulation of key genes involved in either the intrinsic or extrinsic apoptotic pathways. We also demonstrate that trauma-induced disruption of blood-spinal cord barrier function persists for at least 4 days post-injury for compounds up to 10 kDa in size, whereas barrier function is restored for larger molecules within a few hours. This temporary loss of barrier function provides a “
treatment window” through which systemically administered drugs have unrestricted access to spinal tissue in and around the sites of trauma. Taken together, our data provide evidence to support the use of ASIC1a inhibitors as a therapeutic treatment for SCI. This study also emphasizes the importance of objectively grading the functional severity of initial injuries (even when using standardized impacts) and we describe a simple scoring system based on hind limb function that could be adopted in future studies.
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Affiliation(s)
- Liam M Koehn
- Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, Australia
| | - Natassya M Noor
- Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, Australia
| | - Qing Dong
- Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, Australia
| | - Sing-Yan Er
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
| | - Lachlan D Rash
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia; School of Biomedical Sciences, The University of Queensland, St. Lucia, Australia
| | - Glenn F King
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
| | | | - Norman R Saunders
- Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, Australia
| | - Mark D Habgood
- Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, Australia
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12
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Koehn LM, Noor NM, Dong Q, Er SY, Rash LD, King GF, Dziegielewska KM, Saunders NR, Habgood MD. Selective inhibition of ASIC1a confers functional and morphological neuroprotection following traumatic spinal cord injury. F1000Res 2016; 5:1822. [PMID: 28105306 PMCID: PMC5200949 DOI: 10.12688/f1000research.9094.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/29/2016] [Indexed: 11/10/2023] Open
Abstract
Tissue loss after spinal trauma is biphasic, with initial mechanical/haemorrhagic damage at the time of impact being followed by gradual secondary expansion into adjacent, previously unaffected tissue. Limiting the extent of this secondary expansion of tissue damage has the potential to preserve greater residual spinal cord function in patients. The acute tissue hypoxia resulting from spinal cord injury (SCI) activates acid-sensing ion channel 1a (ASIC1a). We surmised that antagonism of this channel should provide neuroprotection and functional preservation after SCI. We show that systemic administration of the spider-venom peptide PcTx1, a selective inhibitor of ASIC1a, improves locomotor function in adult Sprague Dawley rats after thoracic SCI. The degree of functional improvement correlated with the degree of tissue preservation in descending white matter tracts involved in hind limb locomotor function. Transcriptomic analysis suggests that PcTx1-induced preservation of spinal cord tissue does not result from a reduction in apoptosis, with no evidence of down-regulation of key genes involved in either the intrinsic or extrinsic apoptotic pathways. We also demonstrate that trauma-induced disruption of blood-spinal cord barrier function persists for at least 4 days post-injury for compounds up to 10 kDa in size, whereas barrier function is restored for larger molecules within a few hours. This temporary loss of barrier function provides a " treatment window" through which systemically administered drugs have unrestricted access to spinal tissue in and around the sites of trauma. Taken together, our data provide evidence to support the use of ASIC1a inhibitors as a therapeutic treatment for SCI. This study also emphasizes the importance of objectively grading the functional severity of initial injuries (even when using standardized impacts) and we describe a simple scoring system based on hind limb function that could be adopted in future studies.
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Affiliation(s)
- Liam M Koehn
- Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, Australia
| | - Natassya M Noor
- Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, Australia
| | - Qing Dong
- Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, Australia
| | - Sing-Yan Er
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
| | - Lachlan D Rash
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia; School of Biomedical Sciences, The University of Queensland, St. Lucia, Australia
| | - Glenn F King
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
| | | | - Norman R Saunders
- Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, Australia
| | - Mark D Habgood
- Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, Australia
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