Identification of autophagy-related genes in neuropathic pain through bioinformatic analysis
Abstract Background Neuropathic pain (NP) is one of the most common types of chronic pain and significantly compromises the quality of life. Autophagy is an intracellular catabolic process that is required to maintain cellular homeostasis in response to various stresses. The role of autophagy-relate...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-03-01
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| Series: | Hereditas |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s41065-023-00269-w |
| _version_ | 1827983932825534464 |
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| author | Sheng Tian Lanxiang Wu Heqing Zheng Xianhui Zhong Xinping Yu Wei Wu |
| author_facet | Sheng Tian Lanxiang Wu Heqing Zheng Xianhui Zhong Xinping Yu Wei Wu |
| author_sort | Sheng Tian |
| collection | DOAJ |
| description | Abstract Background Neuropathic pain (NP) is one of the most common types of chronic pain and significantly compromises the quality of life. Autophagy is an intracellular catabolic process that is required to maintain cellular homeostasis in response to various stresses. The role of autophagy-related genes in the diagnosis and treatment of neuropathic pain remains unclear. Methods We identified autophagy-related differentially expressed genes (ARDEGs) and differentially expressed miRNAs (DE-miRNAs) in neuropathic pain by bioinformatics analysis of the GSE145226 and GSE145199 datasets. These ARDEGs and their co-expressed genes were subjected to Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, Gene Set Enrichment Analysis (GSEA) and friends analysis. Meanwhile, we constructed TFs-ARDEGs, miRNA-ARDEGs regulatory network through ChIPBase database and the HTFtarget database, multiMir R package. Finally, we performed immune infiltration analysis of ARDEGs by Single Sample Gene Set Enrichment Analysis (ssGSEA). Results We identified 2 potential autophagy-related differentially expressed genes (Sirt2 and ST7) that may be closely associated with the pathogenesis of neuropathic pain. GO, KEGG and GSEA analysis revealed that these two ARDEGs were mainly enriched in pyridine nucleotide metabolic process, nicotinamide nucleotide metabolic process, Nicotinate and nicotinamide metabolism, NF-κB pathway, KRAS signaling, P53 pathway. In the TFs-ARDEGs and miRNA-ARDEGs regulatory network, miR-140-5p and Cebpb were predicted to be as crucial regulators in the progression of NP. For the ssGSEA results, Sirt2 was positively correlated with Eosinophil and Effector memory CD8+ T cell infiltration, which suggested that it may be involved in the regulation of neuroimmune-related signaling. Conclusion Two autophagy-related differentially expressed genes, especially Sirt2, may be potential biomarkers for NP, providing more evidence about the crucial role of autophagy in neuropathic pain. |
| first_indexed | 2024-04-09T22:54:02Z |
| format | Article |
| id | doaj.art-8eb31c482d1a483ba7ebf08efa3f7570 |
| institution | Directory Open Access Journal |
| issn | 1601-5223 |
| language | English |
| last_indexed | 2024-04-09T22:54:02Z |
| publishDate | 2023-03-01 |
| publisher | BMC |
| record_format | Article |
| series | Hereditas |
| spelling | doaj.art-8eb31c482d1a483ba7ebf08efa3f75702023-03-22T11:31:04ZengBMCHereditas1601-52232023-03-01160111610.1186/s41065-023-00269-wIdentification of autophagy-related genes in neuropathic pain through bioinformatic analysisSheng Tian0Lanxiang Wu1Heqing Zheng2Xianhui Zhong3Xinping Yu4Wei Wu5Department of Neurology, The Second Affiliated Hospital of Nanchang UniversityDepartment of Neurology, The Second Affiliated Hospital of Nanchang UniversityDepartment of Neurology, The Second Affiliated Hospital of Nanchang UniversityDepartment of Neurology, The Second Affiliated Hospital of Nanchang UniversityDepartment of Neurology, The Second Affiliated Hospital of Nanchang UniversityDepartment of Neurology, The Second Affiliated Hospital of Nanchang UniversityAbstract Background Neuropathic pain (NP) is one of the most common types of chronic pain and significantly compromises the quality of life. Autophagy is an intracellular catabolic process that is required to maintain cellular homeostasis in response to various stresses. The role of autophagy-related genes in the diagnosis and treatment of neuropathic pain remains unclear. Methods We identified autophagy-related differentially expressed genes (ARDEGs) and differentially expressed miRNAs (DE-miRNAs) in neuropathic pain by bioinformatics analysis of the GSE145226 and GSE145199 datasets. These ARDEGs and their co-expressed genes were subjected to Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, Gene Set Enrichment Analysis (GSEA) and friends analysis. Meanwhile, we constructed TFs-ARDEGs, miRNA-ARDEGs regulatory network through ChIPBase database and the HTFtarget database, multiMir R package. Finally, we performed immune infiltration analysis of ARDEGs by Single Sample Gene Set Enrichment Analysis (ssGSEA). Results We identified 2 potential autophagy-related differentially expressed genes (Sirt2 and ST7) that may be closely associated with the pathogenesis of neuropathic pain. GO, KEGG and GSEA analysis revealed that these two ARDEGs were mainly enriched in pyridine nucleotide metabolic process, nicotinamide nucleotide metabolic process, Nicotinate and nicotinamide metabolism, NF-κB pathway, KRAS signaling, P53 pathway. In the TFs-ARDEGs and miRNA-ARDEGs regulatory network, miR-140-5p and Cebpb were predicted to be as crucial regulators in the progression of NP. For the ssGSEA results, Sirt2 was positively correlated with Eosinophil and Effector memory CD8+ T cell infiltration, which suggested that it may be involved in the regulation of neuroimmune-related signaling. Conclusion Two autophagy-related differentially expressed genes, especially Sirt2, may be potential biomarkers for NP, providing more evidence about the crucial role of autophagy in neuropathic pain.https://doi.org/10.1186/s41065-023-00269-wNeuropathic painAutophagyBioinformatic analysisSirt2 |
| spellingShingle | Sheng Tian Lanxiang Wu Heqing Zheng Xianhui Zhong Xinping Yu Wei Wu Identification of autophagy-related genes in neuropathic pain through bioinformatic analysis Hereditas Neuropathic pain Autophagy Bioinformatic analysis Sirt2 |
| title | Identification of autophagy-related genes in neuropathic pain through bioinformatic analysis |
| title_full | Identification of autophagy-related genes in neuropathic pain through bioinformatic analysis |
| title_fullStr | Identification of autophagy-related genes in neuropathic pain through bioinformatic analysis |
| title_full_unstemmed | Identification of autophagy-related genes in neuropathic pain through bioinformatic analysis |
| title_short | Identification of autophagy-related genes in neuropathic pain through bioinformatic analysis |
| title_sort | identification of autophagy related genes in neuropathic pain through bioinformatic analysis |
| topic | Neuropathic pain Autophagy Bioinformatic analysis Sirt2 |
| url | https://doi.org/10.1186/s41065-023-00269-w |
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