A crucial exosome-related gene pair (AAMP and ABAT) is associated with inflammatory cells in intervertebral disc degeneration
Identification of exosome-related genes (ERGs) and competing endogenous RNAs (ceRNAs) associated with intervertebral disc degeneration (IDD) may improve its diagnosis and reveal its underlying mechanisms. We downloaded 49 samples from Gene Expression Omnibus and identified candidate ERGs using diffe...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-04-01
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| Series: | Frontiers in Immunology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2023.1160801/full |
| _version_ | 1797847170458583040 |
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| author | Huiyong Ren Yumin Li Hao Liu Jiaxin Fan Jie Li Haopeng Li Hongyu Wei Liesu Meng Liesu Meng Shuai Cao |
| author_facet | Huiyong Ren Yumin Li Hao Liu Jiaxin Fan Jie Li Haopeng Li Hongyu Wei Liesu Meng Liesu Meng Shuai Cao |
| author_sort | Huiyong Ren |
| collection | DOAJ |
| description | Identification of exosome-related genes (ERGs) and competing endogenous RNAs (ceRNAs) associated with intervertebral disc degeneration (IDD) may improve its diagnosis and reveal its underlying mechanisms. We downloaded 49 samples from Gene Expression Omnibus and identified candidate ERGs using differentially expressed ERGs (De-ERGs), exosome-related gene pairs (ERGPs), and machine learning algorithms [least absolute shrinkage and selection operator (LASSO) and support vector machine (SVM)]. Immune cell-related ERGs were selected via immune-infiltration analysis, and clinical values were assessed using receiver operating characteristic curves. Based on the De-ERGs, a ceRNA network comprising 1,512 links and 330 nodes was constructed and primarily related to signal transduction pathways, apoptosis-related biological processes, and multiple kinase-related molecular functions. In total, two crucial De-ERGs [angio-associated migratory cell protein (AAMP) and 4-aminobutyrate aminotransferase (ABAT)] were screened from results in De-ERGs, ERGPs, LASSO, and SVM. Increased AAMP expression and decreased ABAT expression were positively and negatively correlated with CD8+ T cell infiltration, respectively. AAMP/ABAT was the only pair differentially expressed in IDD and correlated with CD8+ T cell infiltration. Furthermore, AAMP/ABAT displayed higher accuracy in predicting IDD than individual genes. These results demonstrated the ERGP AAMP/ABAT as a robust signature for identifying IDD and associated with increased CD8+ T cell infiltration, suggesting it as a promising IDD biomarker. |
| first_indexed | 2024-04-09T18:06:56Z |
| format | Article |
| id | doaj.art-8c42e875ad8c4ef991a35717f9e084a9 |
| institution | Directory Open Access Journal |
| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-04-09T18:06:56Z |
| publishDate | 2023-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Immunology |
| spelling | doaj.art-8c42e875ad8c4ef991a35717f9e084a92023-04-14T05:32:03ZengFrontiers Media S.A.Frontiers in Immunology1664-32242023-04-011410.3389/fimmu.2023.11608011160801A crucial exosome-related gene pair (AAMP and ABAT) is associated with inflammatory cells in intervertebral disc degenerationHuiyong Ren0Yumin Li1Hao Liu2Jiaxin Fan3Jie Li4Haopeng Li5Hongyu Wei6Liesu Meng7Liesu Meng8Shuai Cao9Department of Orthopedics, Civil Aviation General Hospital, Beijing, ChinaDepartment of Orthopedics, Civil Aviation General Hospital, Beijing, ChinaDepartment of Orthopaedics, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shanxi, ChinaDepartment of Neurology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, ChinaDepartment of Orthopaedics, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shanxi, ChinaDepartment of Orthopaedics, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shanxi, ChinaDepartment of Orthopaedic Surgery, China-Japan Friendship Hospital, Beijing, ChinaInstitute of Molecular and Translational Medicine (IMTM), and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an, ChinaNational Joint Engineering Research Center of Biodiagnostics and Biotherapy, Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi, ChinaDepartment of Orthopedics, Civil Aviation General Hospital, Beijing, ChinaIdentification of exosome-related genes (ERGs) and competing endogenous RNAs (ceRNAs) associated with intervertebral disc degeneration (IDD) may improve its diagnosis and reveal its underlying mechanisms. We downloaded 49 samples from Gene Expression Omnibus and identified candidate ERGs using differentially expressed ERGs (De-ERGs), exosome-related gene pairs (ERGPs), and machine learning algorithms [least absolute shrinkage and selection operator (LASSO) and support vector machine (SVM)]. Immune cell-related ERGs were selected via immune-infiltration analysis, and clinical values were assessed using receiver operating characteristic curves. Based on the De-ERGs, a ceRNA network comprising 1,512 links and 330 nodes was constructed and primarily related to signal transduction pathways, apoptosis-related biological processes, and multiple kinase-related molecular functions. In total, two crucial De-ERGs [angio-associated migratory cell protein (AAMP) and 4-aminobutyrate aminotransferase (ABAT)] were screened from results in De-ERGs, ERGPs, LASSO, and SVM. Increased AAMP expression and decreased ABAT expression were positively and negatively correlated with CD8+ T cell infiltration, respectively. AAMP/ABAT was the only pair differentially expressed in IDD and correlated with CD8+ T cell infiltration. Furthermore, AAMP/ABAT displayed higher accuracy in predicting IDD than individual genes. These results demonstrated the ERGP AAMP/ABAT as a robust signature for identifying IDD and associated with increased CD8+ T cell infiltration, suggesting it as a promising IDD biomarker.https://www.frontiersin.org/articles/10.3389/fimmu.2023.1160801/fullIntervertebral disc degenerationexosomesmachine learninggene pairsimmune infiltration |
| spellingShingle | Huiyong Ren Yumin Li Hao Liu Jiaxin Fan Jie Li Haopeng Li Hongyu Wei Liesu Meng Liesu Meng Shuai Cao A crucial exosome-related gene pair (AAMP and ABAT) is associated with inflammatory cells in intervertebral disc degeneration Frontiers in Immunology Intervertebral disc degeneration exosomes machine learning gene pairs immune infiltration |
| title | A crucial exosome-related gene pair (AAMP and ABAT) is associated with inflammatory cells in intervertebral disc degeneration |
| title_full | A crucial exosome-related gene pair (AAMP and ABAT) is associated with inflammatory cells in intervertebral disc degeneration |
| title_fullStr | A crucial exosome-related gene pair (AAMP and ABAT) is associated with inflammatory cells in intervertebral disc degeneration |
| title_full_unstemmed | A crucial exosome-related gene pair (AAMP and ABAT) is associated with inflammatory cells in intervertebral disc degeneration |
| title_short | A crucial exosome-related gene pair (AAMP and ABAT) is associated with inflammatory cells in intervertebral disc degeneration |
| title_sort | crucial exosome related gene pair aamp and abat is associated with inflammatory cells in intervertebral disc degeneration |
| topic | Intervertebral disc degeneration exosomes machine learning gene pairs immune infiltration |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2023.1160801/full |
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