Transcriptome Analysis and Single-Cell Sequencing Analysis Constructed the Ubiquitination-Related Signature in Glioma and Identified USP4 as a Novel Biomarker
BackgroundGlioma, the most frequent malignant tumor of the neurological system, has a poor prognosis and treatment problems. Glioma’s tumor microenvironment is also little known.MethodsWe downloaded glioma data from the TCGA database. The patients in the TCGA database were split into two groups, one...
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Frontiers Media S.A.
2022-06-01
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| Series: | Frontiers in Immunology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2022.915709/full |
| _version_ | 1818546412856541184 |
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| author | Qikai Tang Zhengxin Chen Zhengxin Chen Jiaheng Xie Chuangqi Mo Jiacheng Lu Qixiang Zhang Zhangjie Wang Wei Wu Huibo Wang Huibo Wang |
| author_facet | Qikai Tang Zhengxin Chen Zhengxin Chen Jiaheng Xie Chuangqi Mo Jiacheng Lu Qixiang Zhang Zhangjie Wang Wei Wu Huibo Wang Huibo Wang |
| author_sort | Qikai Tang |
| collection | DOAJ |
| description | BackgroundGlioma, the most frequent malignant tumor of the neurological system, has a poor prognosis and treatment problems. Glioma’s tumor microenvironment is also little known.MethodsWe downloaded glioma data from the TCGA database. The patients in the TCGA database were split into two groups, one for training and the other for validation. The ubiquitination genes were then evaluated in glioma using COX and Lasso regression to create a ubiquitination-related signature. We assessed the signature’s predictive usefulness and role in the immune microenvironment after it was generated. Finally, in vitro experiment were utilized to check the expression and function of the signature’s key gene, USP4.ResultsThis signature can be used to categorize glioma patients. Glioma patients can be separated into high-risk and low-risk groups in both the training and validation cohorts, with the high-risk group having a significantly worse prognosis (P<0.05). Following further investigation of the immune microenvironment, it was discovered that this risk grouping could serve as a guide for glioma immunotherapy. The activity, invasion and migration capacity, and colony formation ability of U87-MG and LN229 cell lines were drastically reduced after the important gene USP4 in signature was knocked down in cell tests. Overexpression of USP4 in the A172 cell line, on the other hand, greatly improved clonogenesis, activity, invasion and migration.ConclusionsOur research established a foundation for understanding the role of ubiquitination genes in gliomas and identified USP4 as a possible glioma biomarker. |
| first_indexed | 2024-12-12T07:52:52Z |
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| id | doaj.art-da13c44d32e44f7dbc46fc2de4a03ec1 |
| institution | Directory Open Access Journal |
| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-12-12T07:52:52Z |
| publishDate | 2022-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Immunology |
| spelling | doaj.art-da13c44d32e44f7dbc46fc2de4a03ec12022-12-22T00:32:24ZengFrontiers Media S.A.Frontiers in Immunology1664-32242022-06-011310.3389/fimmu.2022.915709915709Transcriptome Analysis and Single-Cell Sequencing Analysis Constructed the Ubiquitination-Related Signature in Glioma and Identified USP4 as a Novel BiomarkerQikai Tang0Zhengxin Chen1Zhengxin Chen2Jiaheng Xie3Chuangqi Mo4Jiacheng Lu5Qixiang Zhang6Zhangjie Wang7Wei Wu8Huibo Wang9Huibo Wang10Department of Neurosurgery, First Affiliated Hospital of Nanjing Medical University, Nanjing, ChinaDepartment of Neurosurgery, First Affiliated Hospital of Nanjing Medical University, Nanjing, ChinaJiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, ChinaDepartment of Burn and Plastic Surgery, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, ChinaDepartment of Neurosurgery, Pukou Branch of Jiangsu People’s Hospital, Nanjing Pukou District Central Hospital, Nanjing, ChinaDepartment of Neurosurgery, First Affiliated Hospital of Nanjing Medical University, Nanjing, ChinaDepartment of Neurosurgery, First Affiliated Hospital of Nanjing Medical University, Nanjing, ChinaDepartment of Neurosurgery, First Affiliated Hospital of Nanjing Medical University, Nanjing, ChinaDepartment of Neurosurgery, First Affiliated Hospital of Nanjing Medical University, Nanjing, ChinaDepartment of Neurosurgery, First Affiliated Hospital of Nanjing Medical University, Nanjing, ChinaJiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, ChinaBackgroundGlioma, the most frequent malignant tumor of the neurological system, has a poor prognosis and treatment problems. Glioma’s tumor microenvironment is also little known.MethodsWe downloaded glioma data from the TCGA database. The patients in the TCGA database were split into two groups, one for training and the other for validation. The ubiquitination genes were then evaluated in glioma using COX and Lasso regression to create a ubiquitination-related signature. We assessed the signature’s predictive usefulness and role in the immune microenvironment after it was generated. Finally, in vitro experiment were utilized to check the expression and function of the signature’s key gene, USP4.ResultsThis signature can be used to categorize glioma patients. Glioma patients can be separated into high-risk and low-risk groups in both the training and validation cohorts, with the high-risk group having a significantly worse prognosis (P<0.05). Following further investigation of the immune microenvironment, it was discovered that this risk grouping could serve as a guide for glioma immunotherapy. The activity, invasion and migration capacity, and colony formation ability of U87-MG and LN229 cell lines were drastically reduced after the important gene USP4 in signature was knocked down in cell tests. Overexpression of USP4 in the A172 cell line, on the other hand, greatly improved clonogenesis, activity, invasion and migration.ConclusionsOur research established a foundation for understanding the role of ubiquitination genes in gliomas and identified USP4 as a possible glioma biomarker.https://www.frontiersin.org/articles/10.3389/fimmu.2022.915709/fullgliomaubiquitinationbioinformaticssignatureimmunotherapy |
| spellingShingle | Qikai Tang Zhengxin Chen Zhengxin Chen Jiaheng Xie Chuangqi Mo Jiacheng Lu Qixiang Zhang Zhangjie Wang Wei Wu Huibo Wang Huibo Wang Transcriptome Analysis and Single-Cell Sequencing Analysis Constructed the Ubiquitination-Related Signature in Glioma and Identified USP4 as a Novel Biomarker Frontiers in Immunology glioma ubiquitination bioinformatics signature immunotherapy |
| title | Transcriptome Analysis and Single-Cell Sequencing Analysis Constructed the Ubiquitination-Related Signature in Glioma and Identified USP4 as a Novel Biomarker |
| title_full | Transcriptome Analysis and Single-Cell Sequencing Analysis Constructed the Ubiquitination-Related Signature in Glioma and Identified USP4 as a Novel Biomarker |
| title_fullStr | Transcriptome Analysis and Single-Cell Sequencing Analysis Constructed the Ubiquitination-Related Signature in Glioma and Identified USP4 as a Novel Biomarker |
| title_full_unstemmed | Transcriptome Analysis and Single-Cell Sequencing Analysis Constructed the Ubiquitination-Related Signature in Glioma and Identified USP4 as a Novel Biomarker |
| title_short | Transcriptome Analysis and Single-Cell Sequencing Analysis Constructed the Ubiquitination-Related Signature in Glioma and Identified USP4 as a Novel Biomarker |
| title_sort | transcriptome analysis and single cell sequencing analysis constructed the ubiquitination related signature in glioma and identified usp4 as a novel biomarker |
| topic | glioma ubiquitination bioinformatics signature immunotherapy |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2022.915709/full |
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