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Guo Z, Zhao Z, Wang X, Zhou J, Liu J, Plunet W, Ren W, Tian L. Identification of mitophagy-related hub genes during the progression of spinal cord injury by integrated multinomial bioinformatics analysis. Biochem Biophys Rep 2024; 38:101654. [PMID: 38375420 PMCID: PMC10875195 DOI: 10.1016/j.bbrep.2024.101654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/21/2024] Open
Abstract
Spinal cord injury (SCI) is a disturbance of peripheral and central nerve conduction that causes disability in sensory and motor function. Currently, there is no effective treatment for SCI. Mitophagy plays a vital role in mitochondrial quality control during various physiological and pathological processes. The study aimed to elucidate the role of mitophagy and identify potential mitophagy-related hub genes in SCI pathophysiology. Two datasets (GSE15878 and GSE138637) were analyzed. Firstly, the differentially expressed genes (DEGs) were identified and mitophagy-related genes were obtained from GeneCards, then the intersection between SCI and mitophagy-related genes was determined. Next, we performed gene set enrichment analysis (GSEA), weighted gene co-expression network analysis (WGCNA), protein-protein interaction network (PPI network), least absolute shrinkage and selection operator (LASSO), and cluster analysis to identify and define the hub genes in SCI. Finally, the link between hub genes and infiltrating immune cells was investigated and the potential transcriptional regulation/small molecular compounds to target hub genes were predicted. In total, SKP1 and BAP1 were identified as hub genes of mitophagy-related DEGs during SCI development and regulatory T cells (Tregs)/resting NK cells/activated mast cells may play an essential role in the progression of SCI. LINC00324 and SNHG16 may regulate SKP1 and BAP1, respectively, through miRNAs. Eleven and eight transcriptional factors (TFs) regulate SKP1 and BAP1, respectively, and six small molecular compounds target BAP1. Then, the mRNA expression levels of BAP1 and SKP1 were detected in the injured sites of spinal cord of SD rats at 6 h and 72 h after injury using RT-qPCR, and found that the level were decreased. Therefore, the pathways of mitophagy are downregulated during the pathophysiology of SCI, and SKP1 and BAP1 could be accessible targets for diagnosing and treating SCI.
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Affiliation(s)
- Zhihao Guo
- The Department of Orthopedics, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Zihui Zhao
- Institute of Trauma & Orthopedics, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Xiaoge Wang
- Institute of Trauma & Orthopedics, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Jie Zhou
- The Department of Orthopedics, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Jie Liu
- Institute of Trauma & Orthopedics, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
- Clinical Medical Center of Tissue Engineering and Regeneration, Xinxiang Medical University, Xinxiang, Henan, China
| | - Ward Plunet
- International Collaboration on Repair Discoveries (ICORD), Blusson Spinal Cord Center, Vancouver, British Columbia, Canada
| | - Wenjie Ren
- Institute of Trauma & Orthopedics, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
- Clinical Medical Center of Tissue Engineering and Regeneration, Xinxiang Medical University, Xinxiang, Henan, China
| | - Linqiang Tian
- The Department of Orthopedics, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
- Institute of Trauma & Orthopedics, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
- Clinical Medical Center of Tissue Engineering and Regeneration, Xinxiang Medical University, Xinxiang, Henan, China
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Cabrera-Aldana EE, Balderas-Martínez YI, Velázquez-Cruz R, Tovar-y-Romo LB, Sevilla-Montoya R, Martínez-Cruz A, Martinez-Cordero C, Valdés-Flores M, Santamaria-Olmedo M, Hidalgo-Bravo A, Guízar-Sahagún G. Administration of Tamoxifen Can Regulate Changes in Gene Expression during the Acute Phase of Traumatic Spinal Cord Injury. Curr Issues Mol Biol 2023; 45:7476-7491. [PMID: 37754256 PMCID: PMC10529143 DOI: 10.3390/cimb45090472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/28/2023] Open
Abstract
Traumatic spinal cord injury (SCI) causes irreversible damage leading to incapacity. Molecular mechanisms underlying SCI damage are not fully understood, preventing the development of novel therapies. Tamoxifen (TMX) has emerged as a promising therapy. Our aim was to identify transcriptome changes in the acute phase of SCI and the effect of Tamoxifen on those changes in a rat model of SCI. Four groups were considered: (1) Non-injured without TMX (Sham/TMX-), (2) Non-injured with TMX (Sham/TMX+), (3) injured without TMX (SCI/TMX-), and (4) injured with TMX (SCI/TMX+). Tamoxifen was administered intraperitoneally 30 min after injury, and spinal cord tissues were collected 24 h after injury. Clariom S Assays Array was used for transcriptome analysis. After comparing Sham/TMX- versus SCI/TMX-, 708 genes showed differential expression. The enriched pathways were the SCI pathway and pathways related to the inflammatory response. When comparing SCI/TMX- versus SCI/TMX+, only 30 genes showed differential expression, with no pathways enriched. Our results showed differential expression of genes related to the inflammatory response after SCI, and Tamoxifen seems to regulate gene expression changes in Ccr2 and Mmp12. Our study contributes data regarding the potential value of tamoxifen as a therapeutic resource for traumatic SCI during the acute phase.
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Affiliation(s)
- Eibar E. Cabrera-Aldana
- Department of Genomics Medicine, National Institute of Rehabilitation (INR), Calzada Mexico-Xochimilco 289, Arenal de Guadalupe, Mexico City 14389, Mexico; (E.E.C.-A.); (M.V.-F.); (M.S.-O.)
| | - Yalbi I. Balderas-Martínez
- Laboratorio de Biología Computacional, Instituto Nacional de Enfermedades Respiratorias, Ismael Cosío Villegas, Calz. de Tlalpan 4502, Belisario Domínguez Secc 16, Tlalpan, Mexico City 14080, Mexico;
| | - Rafael Velázquez-Cruz
- Genomics of Bone Metabolism Laboratory, National Institute of Genomic Medicine (INMEGEN), Periférico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico;
| | - Luis B. Tovar-y-Romo
- Department of Molecular Neuropathology, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior s/n, Mexico City 04510, Mexico;
| | - Rosalba Sevilla-Montoya
- Reproductive Research and Perinatal Health Department, National Institute of Perinatology, Montes Urales 800, Lomas de Virreyes, Mexico City 11000, Mexico;
| | - Angelina Martínez-Cruz
- Department of Experimental Surgery, Proyecto Camina, A.C. 4430 Calz. Tlalpan, Mexico City 14050, Mexico;
| | - Claudia Martinez-Cordero
- Regional Hospital of High Specialty of the Bajio, Blvd. Milenio 130, Col. San Carlos la Roncha, León 37660, Guanajuato, Mexico;
| | - Margarita Valdés-Flores
- Department of Genomics Medicine, National Institute of Rehabilitation (INR), Calzada Mexico-Xochimilco 289, Arenal de Guadalupe, Mexico City 14389, Mexico; (E.E.C.-A.); (M.V.-F.); (M.S.-O.)
| | - Monica Santamaria-Olmedo
- Department of Genomics Medicine, National Institute of Rehabilitation (INR), Calzada Mexico-Xochimilco 289, Arenal de Guadalupe, Mexico City 14389, Mexico; (E.E.C.-A.); (M.V.-F.); (M.S.-O.)
| | - Alberto Hidalgo-Bravo
- Department of Genomics Medicine, National Institute of Rehabilitation (INR), Calzada Mexico-Xochimilco 289, Arenal de Guadalupe, Mexico City 14389, Mexico; (E.E.C.-A.); (M.V.-F.); (M.S.-O.)
| | - Gabriel Guízar-Sahagún
- Research Unit for Neurological Diseases, Instituto Mexicano del Seguro Social, 330 Avenida Cuauhtémoc, Mexico City 06720, Mexico
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Zeng Z, Li M, Jiang Z, Lan Y, Chen L, Chen Y, Li H, Hui J, Zhang L, Hu X, Xia H. Integrated transcriptomic and metabolomic profiling reveals dysregulation of purine metabolism during the acute phase of spinal cord injury in rats. Front Neurosci 2022; 16:1066528. [PMID: 36507345 PMCID: PMC9727392 DOI: 10.3389/fnins.2022.1066528] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/01/2022] [Indexed: 11/24/2022] Open
Abstract
Introduction Spinal cord injury (SCI) results in drastic dysregulation of microenvironmental metabolism during the acute phase, which greatly affects neural recovery. A better insight into the potential molecular pathways of metabolic dysregulation by multi-omics analysis could help to reveal targets that promote nerve repair and regeneration in the future. Materials and methods We established the SCI model and rats were randomly divided into two groups: the acute-phase SCI (ASCI) group (n = 14, 3 days post-SCI) and the sham group with day-matched periods (n = 14, without SCI). In each group, rats were sacrificed at 3 days post-surgery for histology study (n = 3), metabolome sequencing (n = 5), transcriptome sequencing (n = 3), and quantitative real-time polymerase chain reaction (n = 3). The motor function of rats was evaluated by double-blind Basso, Beattie, and Bresnahan (BBB) Locomotor Scores at 0, 1, 2, 3 days post-SCI in an open field area. Then the transcriptomic and metabolomic data were integrated in SCI model of rat to reveal the underlying molecular pathways of microenvironmental metabolic dysregulation. Results The histology of the microenvironment was significantly altered in ASCI and the locomotor function was significantly reduced in rats. Metabolomics analysis showed that 360 metabolites were highly altered during the acute phase of SCI, of which 310 were up-regulated and 50 were down-regulated, and bioinformatics analysis revealed that these differential metabolites were mainly enriched in arginine and proline metabolism, D-glutamine and D-glutamate metabolism, purine metabolism, biosynthesis of unsaturated fatty acids. Transcriptomics results showed that 5,963 genes were clearly altered, of which 2,848 genes were up-regulated and 3,115 genes were down-regulated, and these differentially expressed genes were mainly involved in response to stimulus, metabolic process, immune system process. Surprisingly, the Integrative analysis revealed significant dysregulation of purine metabolism at both transcriptome and metabolome levels in the acute phase of SCI, with 48 differential genes and 16 differential metabolites involved. Further analysis indicated that dysregulation of purine metabolism could seriously affect the energy metabolism of the injured microenvironment and increase oxidative stress as well as other responses detrimental to nerve repair and regeneration. Discussion On the whole, we have for the first time combined transcriptomics and metabolomics to systematically analyze the potential molecular pathways of metabolic dysregulation in the acute phase of SCI, which will contribute to broaden our understanding of the sophisticated molecular mechanisms of SCI, in parallel with serving as a foundation for future studies of neural repair and regeneration after SCI.
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Affiliation(s)
- Zhong Zeng
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China,Ningxia Key Laboratory of Stem Cell and Regenerative Medicine, General Hospital of Ningxia Medical University, Yinchuan, China,School of Clinical Medicine, Ningxia Medical University, Yinchuan, China,Ningxia Key Laboratory of Craniocerebral Diseases, Ningxia Medical University, Yinchuan, China
| | - Mei Li
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China,Ningxia Key Laboratory of Stem Cell and Regenerative Medicine, General Hospital of Ningxia Medical University, Yinchuan, China,School of Clinical Medicine, Ningxia Medical University, Yinchuan, China,Ningxia Key Laboratory of Craniocerebral Diseases, Ningxia Medical University, Yinchuan, China
| | - Zhanfeng Jiang
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China,Ningxia Key Laboratory of Stem Cell and Regenerative Medicine, General Hospital of Ningxia Medical University, Yinchuan, China,School of Clinical Medicine, Ningxia Medical University, Yinchuan, China
| | - Yuanxiang Lan
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China,Ningxia Key Laboratory of Stem Cell and Regenerative Medicine, General Hospital of Ningxia Medical University, Yinchuan, China,School of Clinical Medicine, Ningxia Medical University, Yinchuan, China
| | - Lei Chen
- Department of Neurosurgery, The First People’s Hospital of Shizuishan, Shizuishan, China
| | - Yanjun Chen
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China,Ningxia Key Laboratory of Stem Cell and Regenerative Medicine, General Hospital of Ningxia Medical University, Yinchuan, China,School of Clinical Medicine, Ningxia Medical University, Yinchuan, China
| | - Hailiang Li
- School of Clinical Medicine, Ningxia Medical University, Yinchuan, China,Ningxia Key Laboratory of Craniocerebral Diseases, Ningxia Medical University, Yinchuan, China
| | - Jianwen Hui
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China,Ningxia Key Laboratory of Stem Cell and Regenerative Medicine, General Hospital of Ningxia Medical University, Yinchuan, China,School of Clinical Medicine, Ningxia Medical University, Yinchuan, China
| | - Lijian Zhang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Hebei University, Baoding, China
| | - Xvlei Hu
- Department of Neurosurgery, Shanxi Provincial People’s Hospital, Taiyuan, China
| | - Hechun Xia
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China,Ningxia Key Laboratory of Stem Cell and Regenerative Medicine, General Hospital of Ningxia Medical University, Yinchuan, China,*Correspondence: Hechun Xia,
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Leemhuis E, Favieri F, Forte G, Pazzaglia M. Integrated Neuroregenerative Techniques for Plasticity of the Injured Spinal Cord. Biomedicines 2022; 10:biomedicines10102563. [PMID: 36289825 PMCID: PMC9599452 DOI: 10.3390/biomedicines10102563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/18/2022] [Accepted: 10/10/2022] [Indexed: 11/16/2022] Open
Abstract
On the slow path to improving the life expectancy and quality of life of patients post spinal cord injury (SCI), recovery remains controversial. The potential role of the regenerative capacity of the nervous system has led to numerous attempts to stimulate the SCI to re-establish the interrupted sensorimotor loop and to understand its potential in the recovery process. Numerous resources are now available, from pharmacological to biomolecular approaches and from neuromodulation to sensorimotor rehabilitation interventions based on the use of various neural interfaces, exoskeletons, and virtual reality applications. The integration of existing resources seems to be a promising field of research, especially from the perspective of improving living conditions in the short to medium term. Goals such as reducing chronic forms of neuropathic pain, regaining control over certain physiological activities, and enhancing residual abilities are often more urgent than complete functional recovery. In this perspective article, we provide an overview of the latest interventions for the treatment of SCI through broad phases of injury rehabilitation. The underlying intention of this work is to introduce a spinal cord neuroplasticity-based multimodal approach to promote functional recovery and improve quality of life after SCI. Nonetheless, when used separately, biomolecular therapeutic approaches have been shown to have modest outcomes.
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Affiliation(s)
- Erik Leemhuis
- Dipartimento di Psicologia, Sapienza Università di Roma, 00185 Rome, Italy
- Body and Action Lab, IRCCS Fondazione Santa Lucia, 00179 Rome, Italy
- Correspondence: (E.L.); (M.P.)
| | - Francesca Favieri
- Dipartimento di Psicologia, Sapienza Università di Roma, 00185 Rome, Italy
- Body and Action Lab, IRCCS Fondazione Santa Lucia, 00179 Rome, Italy
| | - Giuseppe Forte
- Body and Action Lab, IRCCS Fondazione Santa Lucia, 00179 Rome, Italy
- Dipartimento di Psicologia Dinamica, Clinica e Salute, Sapienza Università di Roma, 00185 Roma, Italy
| | - Mariella Pazzaglia
- Dipartimento di Psicologia, Sapienza Università di Roma, 00185 Rome, Italy
- Body and Action Lab, IRCCS Fondazione Santa Lucia, 00179 Rome, Italy
- Correspondence: (E.L.); (M.P.)
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Pang QM, Chen SY, Xu QJ, Zhang M, Liang DF, Fu SP, Yu J, Liu ZL, Zhang Q, Zhang T. Effects of astrocytes and microglia on neuroinflammation after spinal cord injury and related immunomodulatory strategies. Int Immunopharmacol 2022; 108:108754. [PMID: 35397392 DOI: 10.1016/j.intimp.2022.108754] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/14/2022] [Accepted: 03/31/2022] [Indexed: 12/12/2022]
Abstract
Spinal cord injury (SCI) is a catastrophic event which is still without adequate therapies. Neuroinflammation is the main pathogenesis of secondary damage post-SCI, leading to tissue loss and neurological dysfunction. Previous studies have shown that microglia and astrocytes are the major immune cells in the central nervous system (CNS) and play a crucial role in modulating neuroinflammatory responses. In this study, we mainly review the effects of neuroinflammation in SCI, focusing on the contributions of microglia and astrocytes and their cross-talk. Furthermore, we will also discuss therapeutic strategies on how to regulate their immunophenotype to suppress robust inflammation and facilitate injury prognosis.
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Affiliation(s)
- Qi-Ming Pang
- Key Laboratory of Cell Engineering of Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China; Department of Orthopedics, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Si-Yu Chen
- Key Laboratory of Cell Engineering of Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Qi-Jing Xu
- Department of Human Anatomy, Zunyi Medical University, Zunyi, Guizhou, China
| | - Meng Zhang
- Key Laboratory of Cell Engineering of Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Da-Fei Liang
- Department of Human Anatomy, Zunyi Medical University, Zunyi, Guizhou, China
| | - Sheng-Ping Fu
- Key Laboratory of Cell Engineering of Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China; Department of Orthopedics, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Jiang Yu
- Key Laboratory of Cell Engineering of Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Zu-Lin Liu
- Key Laboratory of Cell Engineering of Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Qian Zhang
- Department of Human Anatomy, Zunyi Medical University, Zunyi, Guizhou, China.
| | - Tao Zhang
- Key Laboratory of Cell Engineering of Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China; Department of Orthopedics, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China.
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