Circular RNA Expression Alteration and Bioinformatics Analysis in Rats After Traumatic Spinal Cord Injury
Spinal cord injury (SCI) is mostly caused by trauma. As primary mechanical injury is unavoidable in SCI, a focus on the pathophysiology and underlying molecular mechanisms of SCI-induced secondary injury is necessary to develop promising treatments for SCI patients. Circular RNAs (circRNAs) are asso...
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Frontiers Media S.A.
2019-01-01
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| Series: | Frontiers in Molecular Neuroscience |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fnmol.2018.00497/full |
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| author | Chuan Qin Chuan Qin Chuan Qin Chuan Qin Chuan Qin Chang-Bin Liu Chang-Bin Liu Chang-Bin Liu Chang-Bin Liu Chang-Bin Liu De-Gang Yang De-Gang Yang De-Gang Yang De-Gang Yang De-Gang Yang Feng Gao Feng Gao Feng Gao Feng Gao Feng Gao Xin Zhang Xin Zhang Xin Zhang Xin Zhang Xin Zhang Chao Zhang Chao Zhang Chao Zhang Chao Zhang Chao Zhang Liang-Jie Du Liang-Jie Du Liang-Jie Du Liang-Jie Du Liang-Jie Du Ming-Liang Yang Ming-Liang Yang Ming-Liang Yang Ming-Liang Yang Ming-Liang Yang Jian-Jun Li Jian-Jun Li Jian-Jun Li Jian-Jun Li Jian-Jun Li |
| author_facet | Chuan Qin Chuan Qin Chuan Qin Chuan Qin Chuan Qin Chang-Bin Liu Chang-Bin Liu Chang-Bin Liu Chang-Bin Liu Chang-Bin Liu De-Gang Yang De-Gang Yang De-Gang Yang De-Gang Yang De-Gang Yang Feng Gao Feng Gao Feng Gao Feng Gao Feng Gao Xin Zhang Xin Zhang Xin Zhang Xin Zhang Xin Zhang Chao Zhang Chao Zhang Chao Zhang Chao Zhang Chao Zhang Liang-Jie Du Liang-Jie Du Liang-Jie Du Liang-Jie Du Liang-Jie Du Ming-Liang Yang Ming-Liang Yang Ming-Liang Yang Ming-Liang Yang Ming-Liang Yang Jian-Jun Li Jian-Jun Li Jian-Jun Li Jian-Jun Li Jian-Jun Li |
| author_sort | Chuan Qin |
| collection | DOAJ |
| description | Spinal cord injury (SCI) is mostly caused by trauma. As primary mechanical injury is unavoidable in SCI, a focus on the pathophysiology and underlying molecular mechanisms of SCI-induced secondary injury is necessary to develop promising treatments for SCI patients. Circular RNAs (circRNAs) are associated with various diseases. Nevertheless, studies to date have not yet determined the functional roles of circRNAs in traumatic SCI. We examined circRNA expression profiles in the contused spinal cords of rats using microarray and quantitative reverse transcription-PCR (qRT-PCR) then predict their potential roles in post-SCI pathophysiology with bioinformatics. We found a total of 1676 differentially expressed circRNAs (fold change ≥ 2.0; P < 0.05) in spinal cord 3 days after contusion using circRNA microarray; 1261 circRNAs were significantly downregulated, whereas the remaining 415 were significantly upregulated. Then, five selected circRNAs, namely, rno_circRNA_005342, rno_circRNA_015513, rno_circRNA_002948, rno_circRNA_006096, and rno_circRNA_013017 were all significantly downregulated in the SCI group after verification by qRT-PCR, demonstrating a similar expression pattern in both microarray and PCR data. The next section of the study was concerned with the prediction of circRNA/miRNA/mRNA interactions using bioinformatics analysis. In the final part of the study, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes analyses indicated carbohydrate metabolic process was one of the most significant enrichments and meaningful terms after GO analysis, and the top two signaling pathways affected by the circRNAs-miRNAs axes were the AMP-activated protein kinase signaling pathway and the peroxisome related pathway. In summary, this study showed an altered circRNA expression pattern that may be involved in physiological and pathological processes in rats after traumatic SCI, providing deep insights into numerous possibilities for SCI treatment targets by regulating circRNAs. |
| first_indexed | 2024-12-10T11:26:59Z |
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| issn | 1662-5099 |
| language | English |
| last_indexed | 2024-12-10T11:26:59Z |
| publishDate | 2019-01-01 |
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| series | Frontiers in Molecular Neuroscience |
| spelling | doaj.art-bfa1e3a915c44c68959539b925ca92d52022-12-22T01:50:42ZengFrontiers Media S.A.Frontiers in Molecular Neuroscience1662-50992019-01-011110.3389/fnmol.2018.00497426477Circular RNA Expression Alteration and Bioinformatics Analysis in Rats After Traumatic Spinal Cord InjuryChuan Qin0Chuan Qin1Chuan Qin2Chuan Qin3Chuan Qin4Chang-Bin Liu5Chang-Bin Liu6Chang-Bin Liu7Chang-Bin Liu8Chang-Bin Liu9De-Gang Yang10De-Gang Yang11De-Gang Yang12De-Gang Yang13De-Gang Yang14Feng Gao15Feng Gao16Feng Gao17Feng Gao18Feng Gao19Xin Zhang20Xin Zhang21Xin Zhang22Xin Zhang23Xin Zhang24Chao Zhang25Chao Zhang26Chao Zhang27Chao Zhang28Chao Zhang29Liang-Jie Du30Liang-Jie Du31Liang-Jie Du32Liang-Jie Du33Liang-Jie Du34Ming-Liang Yang35Ming-Liang Yang36Ming-Liang Yang37Ming-Liang Yang38Ming-Liang Yang39Jian-Jun Li40Jian-Jun Li41Jian-Jun Li42Jian-Jun Li43Jian-Jun Li44School of Rehabilitation Medicine, Capital Medical University, Beijing, ChinaChina Rehabilitation Science Institute, Beijing, ChinaCenter of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, ChinaDepartment of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, ChinaBeijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, ChinaSchool of Rehabilitation Medicine, Capital Medical University, Beijing, ChinaChina Rehabilitation Science Institute, Beijing, ChinaCenter of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, ChinaDepartment of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, ChinaBeijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, ChinaSchool of Rehabilitation Medicine, Capital Medical University, Beijing, ChinaChina Rehabilitation Science Institute, Beijing, ChinaCenter of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, ChinaDepartment of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, ChinaBeijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, ChinaSchool of Rehabilitation Medicine, Capital Medical University, Beijing, ChinaChina Rehabilitation Science Institute, Beijing, ChinaCenter of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, ChinaDepartment of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, ChinaBeijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, ChinaSchool of Rehabilitation Medicine, Capital Medical University, Beijing, ChinaChina Rehabilitation Science Institute, Beijing, ChinaCenter of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, ChinaDepartment of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, ChinaBeijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, ChinaSchool of Rehabilitation Medicine, Capital Medical University, Beijing, ChinaChina Rehabilitation Science Institute, Beijing, ChinaCenter of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, ChinaDepartment of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, ChinaBeijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, ChinaSchool of Rehabilitation Medicine, Capital Medical University, Beijing, ChinaChina Rehabilitation Science Institute, Beijing, ChinaCenter of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, ChinaDepartment of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, ChinaBeijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, ChinaSchool of Rehabilitation Medicine, Capital Medical University, Beijing, ChinaChina Rehabilitation Science Institute, Beijing, ChinaCenter of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, ChinaDepartment of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, ChinaBeijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, ChinaSchool of Rehabilitation Medicine, Capital Medical University, Beijing, ChinaChina Rehabilitation Science Institute, Beijing, ChinaCenter of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, ChinaDepartment of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, ChinaBeijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, ChinaSpinal cord injury (SCI) is mostly caused by trauma. As primary mechanical injury is unavoidable in SCI, a focus on the pathophysiology and underlying molecular mechanisms of SCI-induced secondary injury is necessary to develop promising treatments for SCI patients. Circular RNAs (circRNAs) are associated with various diseases. Nevertheless, studies to date have not yet determined the functional roles of circRNAs in traumatic SCI. We examined circRNA expression profiles in the contused spinal cords of rats using microarray and quantitative reverse transcription-PCR (qRT-PCR) then predict their potential roles in post-SCI pathophysiology with bioinformatics. We found a total of 1676 differentially expressed circRNAs (fold change ≥ 2.0; P < 0.05) in spinal cord 3 days after contusion using circRNA microarray; 1261 circRNAs were significantly downregulated, whereas the remaining 415 were significantly upregulated. Then, five selected circRNAs, namely, rno_circRNA_005342, rno_circRNA_015513, rno_circRNA_002948, rno_circRNA_006096, and rno_circRNA_013017 were all significantly downregulated in the SCI group after verification by qRT-PCR, demonstrating a similar expression pattern in both microarray and PCR data. The next section of the study was concerned with the prediction of circRNA/miRNA/mRNA interactions using bioinformatics analysis. In the final part of the study, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes analyses indicated carbohydrate metabolic process was one of the most significant enrichments and meaningful terms after GO analysis, and the top two signaling pathways affected by the circRNAs-miRNAs axes were the AMP-activated protein kinase signaling pathway and the peroxisome related pathway. In summary, this study showed an altered circRNA expression pattern that may be involved in physiological and pathological processes in rats after traumatic SCI, providing deep insights into numerous possibilities for SCI treatment targets by regulating circRNAs.https://www.frontiersin.org/article/10.3389/fnmol.2018.00497/fullcircular RNAspinal cord injurymicroarraybioinformaticsrats |
| spellingShingle | Chuan Qin Chuan Qin Chuan Qin Chuan Qin Chuan Qin Chang-Bin Liu Chang-Bin Liu Chang-Bin Liu Chang-Bin Liu Chang-Bin Liu De-Gang Yang De-Gang Yang De-Gang Yang De-Gang Yang De-Gang Yang Feng Gao Feng Gao Feng Gao Feng Gao Feng Gao Xin Zhang Xin Zhang Xin Zhang Xin Zhang Xin Zhang Chao Zhang Chao Zhang Chao Zhang Chao Zhang Chao Zhang Liang-Jie Du Liang-Jie Du Liang-Jie Du Liang-Jie Du Liang-Jie Du Ming-Liang Yang Ming-Liang Yang Ming-Liang Yang Ming-Liang Yang Ming-Liang Yang Jian-Jun Li Jian-Jun Li Jian-Jun Li Jian-Jun Li Jian-Jun Li Circular RNA Expression Alteration and Bioinformatics Analysis in Rats After Traumatic Spinal Cord Injury Frontiers in Molecular Neuroscience circular RNA spinal cord injury microarray bioinformatics rats |
| title | Circular RNA Expression Alteration and Bioinformatics Analysis in Rats After Traumatic Spinal Cord Injury |
| title_full | Circular RNA Expression Alteration and Bioinformatics Analysis in Rats After Traumatic Spinal Cord Injury |
| title_fullStr | Circular RNA Expression Alteration and Bioinformatics Analysis in Rats After Traumatic Spinal Cord Injury |
| title_full_unstemmed | Circular RNA Expression Alteration and Bioinformatics Analysis in Rats After Traumatic Spinal Cord Injury |
| title_short | Circular RNA Expression Alteration and Bioinformatics Analysis in Rats After Traumatic Spinal Cord Injury |
| title_sort | circular rna expression alteration and bioinformatics analysis in rats after traumatic spinal cord injury |
| topic | circular RNA spinal cord injury microarray bioinformatics rats |
| url | https://www.frontiersin.org/article/10.3389/fnmol.2018.00497/full |
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