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Bioinformatic identification of key candidate genes and pathways in axon regeneration after spinal cord injury in zebrafish
Zebrafish and human genomes are highly homologous; however, despite this genomic similarity, adult zebrafish can achieve neuronal proliferation, regeneration and functional restoration within 6–8 weeks after spinal cord injury, whereas humans cannot. To analyze differentially expressed zebrafish gen...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Wolters Kluwer - Medknow
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6862403/ https://www.ncbi.nlm.nih.gov/pubmed/31535658 http://dx.doi.org/10.4103/1673-5374.264460 |
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author | Li, Jia-He Shi, Zhong-Ju Li, Yan Pan, Bin Yuan, Shi-Yang Shi, Lin-Lin Hao, Yan Cao, Fu-Jiang Feng, Shi-Qing |
author_facet | Li, Jia-He Shi, Zhong-Ju Li, Yan Pan, Bin Yuan, Shi-Yang Shi, Lin-Lin Hao, Yan Cao, Fu-Jiang Feng, Shi-Qing |
author_sort | Li, Jia-He |
collection | PubMed |
description | Zebrafish and human genomes are highly homologous; however, despite this genomic similarity, adult zebrafish can achieve neuronal proliferation, regeneration and functional restoration within 6–8 weeks after spinal cord injury, whereas humans cannot. To analyze differentially expressed zebrafish genes between axon-regenerated neurons and axon-non-regenerated neurons after spinal cord injury, and to explore the key genes and pathways of axonal regeneration after spinal cord injury, microarray GSE56842 was analyzed using the online tool, GEO2R, in the Gene Expression Omnibus database. Gene ontology and protein-protein interaction networks were used to analyze the identified differentially expressed genes. Finally, we screened for genes and pathways that may play a role in spinal cord injury repair in zebrafish and mammals. A total of 636 differentially expressed genes were obtained, including 255 up-regulated and 381 down-regulated differentially expressed genes in axon-regenerated neurons. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment results were also obtained. A protein-protein interaction network contained 480 node genes and 1976 node connections. We also obtained the 10 hub genes with the highest correlation and the two modules with the highest score. The results showed that spectrin may promote axonal regeneration after spinal cord injury in zebrafish. Transforming growth factor beta signaling may inhibit repair after spinal cord injury in zebrafish. Focal adhesion or tight junctions may play an important role in the migration and proliferation of some cells, such as Schwann cells or neural progenitor cells, after spinal cord injury in zebrafish. Bioinformatic analysis identified key candidate genes and pathways in axonal regeneration after spinal cord injury in zebrafish, providing targets for treatment of spinal cord injury in mammals. |
format | Online Article Text |
id | pubmed-6862403 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Wolters Kluwer - Medknow |
record_format | MEDLINE/PubMed |
spelling | pubmed-68624032020-01-02 Bioinformatic identification of key candidate genes and pathways in axon regeneration after spinal cord injury in zebrafish Li, Jia-He Shi, Zhong-Ju Li, Yan Pan, Bin Yuan, Shi-Yang Shi, Lin-Lin Hao, Yan Cao, Fu-Jiang Feng, Shi-Qing Neural Regen Res Research Article Zebrafish and human genomes are highly homologous; however, despite this genomic similarity, adult zebrafish can achieve neuronal proliferation, regeneration and functional restoration within 6–8 weeks after spinal cord injury, whereas humans cannot. To analyze differentially expressed zebrafish genes between axon-regenerated neurons and axon-non-regenerated neurons after spinal cord injury, and to explore the key genes and pathways of axonal regeneration after spinal cord injury, microarray GSE56842 was analyzed using the online tool, GEO2R, in the Gene Expression Omnibus database. Gene ontology and protein-protein interaction networks were used to analyze the identified differentially expressed genes. Finally, we screened for genes and pathways that may play a role in spinal cord injury repair in zebrafish and mammals. A total of 636 differentially expressed genes were obtained, including 255 up-regulated and 381 down-regulated differentially expressed genes in axon-regenerated neurons. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment results were also obtained. A protein-protein interaction network contained 480 node genes and 1976 node connections. We also obtained the 10 hub genes with the highest correlation and the two modules with the highest score. The results showed that spectrin may promote axonal regeneration after spinal cord injury in zebrafish. Transforming growth factor beta signaling may inhibit repair after spinal cord injury in zebrafish. Focal adhesion or tight junctions may play an important role in the migration and proliferation of some cells, such as Schwann cells or neural progenitor cells, after spinal cord injury in zebrafish. Bioinformatic analysis identified key candidate genes and pathways in axonal regeneration after spinal cord injury in zebrafish, providing targets for treatment of spinal cord injury in mammals. Wolters Kluwer - Medknow 2019-09-16 /pmc/articles/PMC6862403/ /pubmed/31535658 http://dx.doi.org/10.4103/1673-5374.264460 Text en Copyright: © Neural Regeneration Research http://creativecommons.org/licenses/by-nc-sa/4.0 This is an open access journal, and articles are distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 License, which allows others to remix, tweak, and build upon the work non-commercially, as long as appropriate credit is given and the new creations are licensed under the identical terms. |
spellingShingle | Research Article Li, Jia-He Shi, Zhong-Ju Li, Yan Pan, Bin Yuan, Shi-Yang Shi, Lin-Lin Hao, Yan Cao, Fu-Jiang Feng, Shi-Qing Bioinformatic identification of key candidate genes and pathways in axon regeneration after spinal cord injury in zebrafish |
title | Bioinformatic identification of key candidate genes and pathways in axon regeneration after spinal cord injury in zebrafish |
title_full | Bioinformatic identification of key candidate genes and pathways in axon regeneration after spinal cord injury in zebrafish |
title_fullStr | Bioinformatic identification of key candidate genes and pathways in axon regeneration after spinal cord injury in zebrafish |
title_full_unstemmed | Bioinformatic identification of key candidate genes and pathways in axon regeneration after spinal cord injury in zebrafish |
title_short | Bioinformatic identification of key candidate genes and pathways in axon regeneration after spinal cord injury in zebrafish |
title_sort | bioinformatic identification of key candidate genes and pathways in axon regeneration after spinal cord injury in zebrafish |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6862403/ https://www.ncbi.nlm.nih.gov/pubmed/31535658 http://dx.doi.org/10.4103/1673-5374.264460 |
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