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Shen W, Cai J, Li J, Li W, Shi P, Zhao X, Feng S. Regulation of MicroRNAs After Spinal Cord Injury in Adult Zebrafish. J Mol Neurosci 2024; 74:66. [PMID: 38990400 DOI: 10.1007/s12031-024-02242-2] [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: 06/09/2024] [Accepted: 07/01/2024] [Indexed: 07/12/2024]
Abstract
Spinal cord injury (SCI) is a central nerve injury that often leads to loss of motor and sensory functions at or below the level of the injury. Zebrafish have a strong ability to repair after SCI, but the role of microRNAs (miRNAs) after SCI remains unclear. Locomotor behavior analysis showed that adult zebrafish recovered about 30% of their motor ability at 2 weeks and 55% at 3 weeks after SCI, reflecting their strong ability to repair SCI. Through miRNA sequencing, mRNA sequencing, RT-qPCR experiment verification, and bioinformatics predictive analysis, the key miRNAs and related genes in the repair of SCI were screened. A total of 38 miRNAs were significantly different, the top ten miRNAs were verified by RT-qPCR. The prediction target genes were verified by the mRNAs sequencing results at the same time point. Finally, 182 target genes were identified as likely to be networked regulated by the 38 different miRNAs. GO and KEGG enrichment analysis found that miRNAs targeted gene regulation of many key pathways, such as membrane tissue transport, ribosome function, lipid binding, and peroxidase activity. The PPI network analysis showed that miRNAs were involved in SCI repair through complex network regulation, among which dre-miR-21 may enhance cell reversibility through nop56, and that dre-miR-125c regulates axon growth through kpnb1 to repair SCI.
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Affiliation(s)
- Wenyuan Shen
- Department of Orthopedics, the Second Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, 247 Beiyuan Street, Jinan, Shandong, 250033, China
- International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord, Department of Orthopedics, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China
| | - Jun Cai
- Tianjin Medicine and Health Research Center, Tianjin Institute of Medical & Pharmaceutical Sciences, Tianjin, 300020, China
| | - Jinze Li
- International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord, Department of Orthopedics, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China.
| | - Wenchang Li
- Tianjin Medicine and Health Research Center, Tianjin Institute of Medical & Pharmaceutical Sciences, Tianjin, 300020, China
| | - Pengcheng Shi
- Tianjin Medicine and Health Research Center, Tianjin Institute of Medical & Pharmaceutical Sciences, Tianjin, 300020, China
| | - Xiumei Zhao
- Tianjin Medicine and Health Research Center, Tianjin Institute of Medical & Pharmaceutical Sciences, Tianjin, 300020, China.
| | - Shiqing Feng
- Department of Orthopedics, the Second Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, 247 Beiyuan Street, Jinan, Shandong, 250033, China.
- International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord, Department of Orthopedics, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China.
- Orthopedic Research Center of Shandong University &Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.
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Jiang Y, Cai Y, Yang N, Gao S, Li Q, Pang Y, Su P. Molecular mechanisms of spinal cord injury repair across vertebrates: A comparative review. Eur J Neurosci 2024. [PMID: 38978308 DOI: 10.1111/ejn.16462] [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: 11/16/2023] [Revised: 05/09/2024] [Accepted: 06/20/2024] [Indexed: 07/10/2024]
Abstract
In humans and other adult mammals, axon regeneration is difficult in axotomized neurons. Therefore, spinal cord injury (SCI) is a devastating event that can lead to permanent loss of locomotor and sensory functions. Moreover, the molecular mechanisms of axon regeneration in vertebrates are not very well understood, and currently, no effective treatment is available for SCI. In striking contrast to adult mammals, many nonmammalian vertebrates such as reptiles, amphibians, bony fishes and lampreys can spontaneously resume locomotion even after complete SCI. In recent years, rapid progress in the development of next-generation sequencing technologies has offered valuable information on SCI. In this review, we aimed to provide a comparison of axon regeneration process across classical model organisms, focusing on crucial genes and signalling pathways that play significant roles in the regeneration of individually identifiable descending neurons after SCI. Considering the special evolutionary location and powerful regenerative ability of lamprey and zebrafish, they will be the key model organisms for ongoing studies on spinal cord regeneration. Detailed study of SCI in these model organisms will help in the elucidation of molecular mechanisms of neuron regeneration across species.
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Affiliation(s)
- Ying Jiang
- College of Life Science, Liaoning Normal University, Dalian, China
- Lamprey Research Center, Liaoning Normal University, Dalian, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Yang Cai
- College of Life Science, Liaoning Normal University, Dalian, China
- Lamprey Research Center, Liaoning Normal University, Dalian, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Ning Yang
- College of Life Science, Liaoning Normal University, Dalian, China
- Lamprey Research Center, Liaoning Normal University, Dalian, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Si Gao
- College of Life Science, Liaoning Normal University, Dalian, China
- Lamprey Research Center, Liaoning Normal University, Dalian, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Qingwei Li
- College of Life Science, Liaoning Normal University, Dalian, China
- Lamprey Research Center, Liaoning Normal University, Dalian, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Yue Pang
- College of Life Science, Liaoning Normal University, Dalian, China
- Lamprey Research Center, Liaoning Normal University, Dalian, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Peng Su
- College of Life Science, Liaoning Normal University, Dalian, China
- Lamprey Research Center, Liaoning Normal University, Dalian, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
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Davis G, Hameister B, Dunnum C, Vanderpas E, Carter B. Incorporating Primer Amplification Efficiencies in Quantitative Reverse Transcription Polymerase Chain Reaction Experiments; Considerations for Differential Gene Expression Analyses in Zebrafish. Zebrafish 2023; 20:189-199. [PMID: 37722027 DOI: 10.1089/zeb.2023.0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023] Open
Abstract
Quantitative reverse transcription polymerase chain reaction (RT-qPCR) is commonly used to measure the mRNA expression of target genes in zebrafish. Gene expression values from RT-qPCR are typically reported as relative fold-changes, and relative quantification of RT-qPCR data incorporates primer amplification efficiency values for each target gene. We describe the influence of the primer amplification efficiency analysis method on RT-qPCR gene expression fold-change calculations. This report describes (1) a sample analysis demonstrating incorporation of primer amplification efficiency into RT-qPCR analysis for comparing gene expression of a gene of interest between two groups when normalized to multiple reference genes, (2) the influence of differences in primer amplification efficiencies between measured genes on gene expression differences calculated from theoretical delta-Cq (dCq) values, and (3) an empirical comparison of the influence of three methods of defining primer amplification efficiency in gene expression analyses (delta-delta-Cq [ddCq], standard curve, LinRegPCR) using mRNA measurements of a set of genes in zebrafish embryonic development. Given the need to account for the influence of primer amplification efficiency along with the simplicity of using software programs (LinRegPCR) to measure primer amplification efficiency from RT-qPCR data, we encourage using empirical measurements of primer amplification efficiency for RT-qPCR analysis of differential gene expression in zebrafish.
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Affiliation(s)
- Gillian Davis
- Department of Biology, University of Wisconsin Eau Claire, Eau Claire, Wisconsin, USA
| | - Brianna Hameister
- Department of Biology, University of Wisconsin Eau Claire, Eau Claire, Wisconsin, USA
| | - Cora Dunnum
- Department of Biology, University of Wisconsin Eau Claire, Eau Claire, Wisconsin, USA
| | - Emily Vanderpas
- Department of Biology, University of Wisconsin Eau Claire, Eau Claire, Wisconsin, USA
| | - Brad Carter
- Department of Biology, University of Wisconsin Eau Claire, Eau Claire, Wisconsin, USA
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Cacialli P, Ricci S, Lazzari M, Milani L, Franceschini V. Transcription Pattern of Neurotrophic Factors and Their Receptors in Adult Zebrafish Spinal Cord. Int J Mol Sci 2023; 24:10953. [PMID: 37446129 DOI: 10.3390/ijms241310953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
In vertebrates, neurotrophins and their receptors play a fundamental role in the central and peripheral nervous systems. Several studies reported that each neurotrophin/receptor signalling pathway can perform various functions during axon development, neuronal growth, and plasticity. Previous investigations in some fish species have identified neurotrophins and their receptors in the spinal cord under physiological conditions and after injuries, highlighting their potential role during regeneration. In our study, for the first time, we used an excellent animal model, the zebrafish (Danio rerio), to compare the mRNA localization patterns of neurotrophins and receptors in the spinal cord. We quantified the levels of mRNA using qPCR, and identified the transcription pattern of each neurotrophin/receptor pathway via in situ hybridization. Our data show that ngf/trka are the most transcribed members in the adult zebrafish spinal cord.
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Affiliation(s)
- Pietro Cacialli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
| | - Serena Ricci
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
| | - Maurizio Lazzari
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
| | - Liliana Milani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
| | - Valeria Franceschini
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
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Ren DL, Hu B, Shao GJ, Wang XL, Wei ML. DUSP2 deletion with CRISPR/Cas9 promotes Mauthner cell axonal regeneration at the early stage of zebrafish. Neural Regen Res 2023; 18:577-581. [DOI: 10.4103/1673-5374.350208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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