Integrated analyses reveal evolutionarily conserved and specific injury response genes in dorsal root ganglion
Abstract Rodent dorsal root ganglion (DRG) is widely used for studying axonal injury. Extensive studies have explored genome-wide profiles on rodent DRGs under peripheral nerve insults. However, systematic integration and exploration of these data still be limited. Herein, we re-analyzed 21 RNA-seq...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2022-11-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-022-01783-8 |
| _version_ | 1797984611602530304 |
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| author | Lian Xu Zhifeng Chen Xiaodi Li Hui Xu Yu Zhang Weiwei Yang Jing Chen Shuqiang Zhang Lingchi Xu Songlin Zhou Guicai Li Bin Yu Xiaosong Gu Jian Yang |
| author_facet | Lian Xu Zhifeng Chen Xiaodi Li Hui Xu Yu Zhang Weiwei Yang Jing Chen Shuqiang Zhang Lingchi Xu Songlin Zhou Guicai Li Bin Yu Xiaosong Gu Jian Yang |
| author_sort | Lian Xu |
| collection | DOAJ |
| description | Abstract Rodent dorsal root ganglion (DRG) is widely used for studying axonal injury. Extensive studies have explored genome-wide profiles on rodent DRGs under peripheral nerve insults. However, systematic integration and exploration of these data still be limited. Herein, we re-analyzed 21 RNA-seq datasets and presented a web-based resource (DRGProfile). We identified 53 evolutionarily conserved injury response genes, including well-known injury genes (Atf3, Npy and Gal) and less-studied transcriptional factors (Arid5a, Csrnp1, Zfp367). Notably, we identified species-preference injury response candidates (e.g. Gpr151, Lipn, Anxa10 in mice; Crisp3, Csrp3, Vip, Hamp in rats). Temporal profile analysis reveals expression patterns of genes related to pre-regenerative and regenerating states. Finally, we found a large sex difference in response to sciatic nerve injury, and identified four male-specific markers (Uty, Eif2s3y, Kdm5d, Ddx3y) expressed in DRG. Our study provides a comprehensive integrated landscape for expression change in DRG upon injury which will greatly contribute to the neuroscience community. |
| first_indexed | 2024-04-11T07:05:39Z |
| format | Article |
| id | doaj.art-5f1affe364944f809d585a4630d93612 |
| institution | Directory Open Access Journal |
| issn | 2052-4463 |
| language | English |
| last_indexed | 2024-04-11T07:05:39Z |
| publishDate | 2022-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj.art-5f1affe364944f809d585a4630d936122022-12-22T04:38:25ZengNature PortfolioScientific Data2052-44632022-11-019111610.1038/s41597-022-01783-8Integrated analyses reveal evolutionarily conserved and specific injury response genes in dorsal root ganglionLian Xu0Zhifeng Chen1Xiaodi Li2Hui Xu3Yu Zhang4Weiwei Yang5Jing Chen6Shuqiang Zhang7Lingchi Xu8Songlin Zhou9Guicai Li10Bin Yu11Xiaosong Gu12Jian Yang13Key Laboratory of Neuroregeneration, Ministry of Education and Jiangsu Province, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong UniversityKey Laboratory of Neuroregeneration, Ministry of Education and Jiangsu Province, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong UniversityNanjing University of Chinese MedicineNantong Institute of Genetics and Reproductive Medicine, Affiliated Maternity and Child Healthcare Hospital of Nantong UniversityNanjing University of Chinese MedicineNanjing University of Chinese MedicineKey Laboratory of Neuroregeneration, Ministry of Education and Jiangsu Province, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong UniversityKey Laboratory of Neuroregeneration, Ministry of Education and Jiangsu Province, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong UniversityKey Laboratory of Neuroregeneration, Ministry of Education and Jiangsu Province, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong UniversityKey Laboratory of Neuroregeneration, Ministry of Education and Jiangsu Province, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong UniversityKey Laboratory of Neuroregeneration, Ministry of Education and Jiangsu Province, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong UniversityKey Laboratory of Neuroregeneration, Ministry of Education and Jiangsu Province, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong UniversityKey Laboratory of Neuroregeneration, Ministry of Education and Jiangsu Province, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong UniversityKey Laboratory of Neuroregeneration, Ministry of Education and Jiangsu Province, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong UniversityAbstract Rodent dorsal root ganglion (DRG) is widely used for studying axonal injury. Extensive studies have explored genome-wide profiles on rodent DRGs under peripheral nerve insults. However, systematic integration and exploration of these data still be limited. Herein, we re-analyzed 21 RNA-seq datasets and presented a web-based resource (DRGProfile). We identified 53 evolutionarily conserved injury response genes, including well-known injury genes (Atf3, Npy and Gal) and less-studied transcriptional factors (Arid5a, Csrnp1, Zfp367). Notably, we identified species-preference injury response candidates (e.g. Gpr151, Lipn, Anxa10 in mice; Crisp3, Csrp3, Vip, Hamp in rats). Temporal profile analysis reveals expression patterns of genes related to pre-regenerative and regenerating states. Finally, we found a large sex difference in response to sciatic nerve injury, and identified four male-specific markers (Uty, Eif2s3y, Kdm5d, Ddx3y) expressed in DRG. Our study provides a comprehensive integrated landscape for expression change in DRG upon injury which will greatly contribute to the neuroscience community.https://doi.org/10.1038/s41597-022-01783-8 |
| spellingShingle | Lian Xu Zhifeng Chen Xiaodi Li Hui Xu Yu Zhang Weiwei Yang Jing Chen Shuqiang Zhang Lingchi Xu Songlin Zhou Guicai Li Bin Yu Xiaosong Gu Jian Yang Integrated analyses reveal evolutionarily conserved and specific injury response genes in dorsal root ganglion Scientific Data |
| title | Integrated analyses reveal evolutionarily conserved and specific injury response genes in dorsal root ganglion |
| title_full | Integrated analyses reveal evolutionarily conserved and specific injury response genes in dorsal root ganglion |
| title_fullStr | Integrated analyses reveal evolutionarily conserved and specific injury response genes in dorsal root ganglion |
| title_full_unstemmed | Integrated analyses reveal evolutionarily conserved and specific injury response genes in dorsal root ganglion |
| title_short | Integrated analyses reveal evolutionarily conserved and specific injury response genes in dorsal root ganglion |
| title_sort | integrated analyses reveal evolutionarily conserved and specific injury response genes in dorsal root ganglion |
| url | https://doi.org/10.1038/s41597-022-01783-8 |
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