Identifying Prognostic Biomarkers Related to m6A Modification and Immune Infiltration in Renal Cell Carcinoma
Background: Renal cell carcinoma (RCC) is the largest category of kidney tumors and usually does not have a good prognosis. N6-methyladenosine(m6A) and immune infiltration have received increased attention because of their great influence on the clinical outcome and prognosis of cancer patients. Met...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-11-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/13/11/2059 |
| _version_ | 1797468161860173824 |
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| author | Junjie Ye Peng Li Huijiang Zhang Qi Wu Dongrong Yang |
| author_facet | Junjie Ye Peng Li Huijiang Zhang Qi Wu Dongrong Yang |
| author_sort | Junjie Ye |
| collection | DOAJ |
| description | Background: Renal cell carcinoma (RCC) is the largest category of kidney tumors and usually does not have a good prognosis. N6-methyladenosine(m6A) and immune infiltration have received increased attention because of their great influence on the clinical outcome and prognosis of cancer patients. Methods: We identified hub genes through multi-dimensional screening, including DEGs, PPI analysis, LASSO regression, and random forest. Meanwhile, GO/KEGG enrichment, cMAP analysis, prognostic analysis, m6A prediction, and immune infiltration analysis were performed to understand the potential mechanism and screen therapeutic drugs. Results: We screened 275 downregulated and 185 upregulated genes using three GEO datasets and the TCGA dataset. In total, 82 candidate hub genes were selected using STRING and Cytoscape. Enrichment analysis illustrated that the top 3 biological process terms and top 1 KEGG term were related to immunity. cMAP analysis showed some antagonistic molecules can be candidate drugs for the treatment of RCC. Then, six hub genes (ERBB2, CASR, P2RY8, CAT, PLAUR, and TIMP1) with strong predictive values for prognosis and clinicopathological features were selected. Meanwhile, P2RY8, ERBB2, CAT, and TIMP1 may obtain m6A modification by binding METTL3 or METTL14. On the other hand, differential expression of CAT, ERBB2, P2RY8, PLAUR, and TIMP1 affects the infiltration of the majority of immune cells. Conclusions: We identified six hub genes through multi-dimensional screening. They all possess strong predictive value for prognosis and clinicopathological features. Meanwhile, hub genes may regulate the progression of RCC via an m6A- and immunity-dependent mechanism. |
| first_indexed | 2024-03-09T19:03:38Z |
| format | Article |
| id | doaj.art-8b992399b5b3411793d82a208ae5b202 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T19:03:38Z |
| publishDate | 2022-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-8b992399b5b3411793d82a208ae5b2022023-11-24T04:49:06ZengMDPI AGGenes2073-44252022-11-011311205910.3390/genes13112059Identifying Prognostic Biomarkers Related to m6A Modification and Immune Infiltration in Renal Cell CarcinomaJunjie Ye0Peng Li1Huijiang Zhang2Qi Wu3Dongrong Yang4The Second Affiliated Hospital of Soochow University, Suzhou 215000, ChinaLishui City People’s Hospital, Lishui 323000, ChinaLishui City People’s Hospital, Lishui 323000, ChinaLishui City People’s Hospital, Lishui 323000, ChinaThe Second Affiliated Hospital of Soochow University, Suzhou 215000, ChinaBackground: Renal cell carcinoma (RCC) is the largest category of kidney tumors and usually does not have a good prognosis. N6-methyladenosine(m6A) and immune infiltration have received increased attention because of their great influence on the clinical outcome and prognosis of cancer patients. Methods: We identified hub genes through multi-dimensional screening, including DEGs, PPI analysis, LASSO regression, and random forest. Meanwhile, GO/KEGG enrichment, cMAP analysis, prognostic analysis, m6A prediction, and immune infiltration analysis were performed to understand the potential mechanism and screen therapeutic drugs. Results: We screened 275 downregulated and 185 upregulated genes using three GEO datasets and the TCGA dataset. In total, 82 candidate hub genes were selected using STRING and Cytoscape. Enrichment analysis illustrated that the top 3 biological process terms and top 1 KEGG term were related to immunity. cMAP analysis showed some antagonistic molecules can be candidate drugs for the treatment of RCC. Then, six hub genes (ERBB2, CASR, P2RY8, CAT, PLAUR, and TIMP1) with strong predictive values for prognosis and clinicopathological features were selected. Meanwhile, P2RY8, ERBB2, CAT, and TIMP1 may obtain m6A modification by binding METTL3 or METTL14. On the other hand, differential expression of CAT, ERBB2, P2RY8, PLAUR, and TIMP1 affects the infiltration of the majority of immune cells. Conclusions: We identified six hub genes through multi-dimensional screening. They all possess strong predictive value for prognosis and clinicopathological features. Meanwhile, hub genes may regulate the progression of RCC via an m6A- and immunity-dependent mechanism.https://www.mdpi.com/2073-4425/13/11/2059renal cell carcinomabiomarkerimmune infiltrationm6A modification |
| spellingShingle | Junjie Ye Peng Li Huijiang Zhang Qi Wu Dongrong Yang Identifying Prognostic Biomarkers Related to m6A Modification and Immune Infiltration in Renal Cell Carcinoma Genes renal cell carcinoma biomarker immune infiltration m6A modification |
| title | Identifying Prognostic Biomarkers Related to m6A Modification and Immune Infiltration in Renal Cell Carcinoma |
| title_full | Identifying Prognostic Biomarkers Related to m6A Modification and Immune Infiltration in Renal Cell Carcinoma |
| title_fullStr | Identifying Prognostic Biomarkers Related to m6A Modification and Immune Infiltration in Renal Cell Carcinoma |
| title_full_unstemmed | Identifying Prognostic Biomarkers Related to m6A Modification and Immune Infiltration in Renal Cell Carcinoma |
| title_short | Identifying Prognostic Biomarkers Related to m6A Modification and Immune Infiltration in Renal Cell Carcinoma |
| title_sort | identifying prognostic biomarkers related to m6a modification and immune infiltration in renal cell carcinoma |
| topic | renal cell carcinoma biomarker immune infiltration m6A modification |
| url | https://www.mdpi.com/2073-4425/13/11/2059 |
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