Identification of the Prognosis-Related lncRNAs and Genes in Gastric Cancer
Gastric cancer is a common malignant tumor with high occurrence and recurrence and is the leading cause of death worldwide. However, the prognostic value of protein-coding and non-coding RNAs in stage III gastric cancer has not been systematically analyzed. In this study, using TCGA data, we identif...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-02-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2020.00027/full |
| _version_ | 1818511657846964224 |
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| author | Xiaohui Su Jianjun Zhang Wei Yang Yanqing Liu Yang Liu Zexing Shan Wentao Wang |
| author_facet | Xiaohui Su Jianjun Zhang Wei Yang Yanqing Liu Yang Liu Zexing Shan Wentao Wang |
| author_sort | Xiaohui Su |
| collection | DOAJ |
| description | Gastric cancer is a common malignant tumor with high occurrence and recurrence and is the leading cause of death worldwide. However, the prognostic value of protein-coding and non-coding RNAs in stage III gastric cancer has not been systematically analyzed. In this study, using TCGA data, we identified 585 long noncoding RNAs (lncRNAs) and 927 protein-coding genes (PCGs) correlated with the overall survival rate of gastric cancer. Functional enrichment analysis revealed that the prognostic genes positively correlated with death rates were enriched in pathways, including gap junction, focal adhesion, cell adhesion molecules (CAMs), and neuroactive ligand-receptor interaction, that are involved in the tumor microenvironment and cell-cell communications, suggesting that their dysregulation may promote the tumor progression. To evaluate the performance of the prognostic genes in risk prediction, we built three multivariable Cox models based on prognostic genes selected from the prognostic PCGs and lncRNAs. The performance of the three models based on features from only PCGs or lncRNAs or from all prognostic genes were systematically compared, which revealed that the features selected from all the prognostic genes showed higher performance than the features selected only from lncRNAs or PCGs. Furthermore, the multivariable Cox regression analysis revealed that the stratification with the highest performance was an independent prognostic factor in stage III gastric cancer. In addition, we explored the underlying mechanism of the prognostic lncRNAs in the Cox model by predicting the lncRNA and protein interaction. Specifically, CTD-2218G20.2 was predicted to interact with PSG4, PSG5, and PSG7, which could also interact with cancer-related proteins, including KISS1, TIMP2, MMP11, IGFBP1, EGFR, and CDKN1C, suggesting that CTD-2218G20.2 might participate in the cancer progression via these cancer-related proteins. In summary, the systematic analysis of the prognostic lncRNAs and PCGs was of great importance to the understanding of the progression of stage III gastric cancer. |
| first_indexed | 2024-12-10T23:36:01Z |
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| id | doaj.art-f860c6cd3f1f48c0ba85a494b2953a4c |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-10T23:36:01Z |
| publishDate | 2020-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-f860c6cd3f1f48c0ba85a494b2953a4c2022-12-22T01:29:11ZengFrontiers Media S.A.Frontiers in Genetics1664-80212020-02-011110.3389/fgene.2020.00027510746Identification of the Prognosis-Related lncRNAs and Genes in Gastric CancerXiaohui SuJianjun ZhangWei YangYanqing LiuYang LiuZexing ShanWentao WangGastric cancer is a common malignant tumor with high occurrence and recurrence and is the leading cause of death worldwide. However, the prognostic value of protein-coding and non-coding RNAs in stage III gastric cancer has not been systematically analyzed. In this study, using TCGA data, we identified 585 long noncoding RNAs (lncRNAs) and 927 protein-coding genes (PCGs) correlated with the overall survival rate of gastric cancer. Functional enrichment analysis revealed that the prognostic genes positively correlated with death rates were enriched in pathways, including gap junction, focal adhesion, cell adhesion molecules (CAMs), and neuroactive ligand-receptor interaction, that are involved in the tumor microenvironment and cell-cell communications, suggesting that their dysregulation may promote the tumor progression. To evaluate the performance of the prognostic genes in risk prediction, we built three multivariable Cox models based on prognostic genes selected from the prognostic PCGs and lncRNAs. The performance of the three models based on features from only PCGs or lncRNAs or from all prognostic genes were systematically compared, which revealed that the features selected from all the prognostic genes showed higher performance than the features selected only from lncRNAs or PCGs. Furthermore, the multivariable Cox regression analysis revealed that the stratification with the highest performance was an independent prognostic factor in stage III gastric cancer. In addition, we explored the underlying mechanism of the prognostic lncRNAs in the Cox model by predicting the lncRNA and protein interaction. Specifically, CTD-2218G20.2 was predicted to interact with PSG4, PSG5, and PSG7, which could also interact with cancer-related proteins, including KISS1, TIMP2, MMP11, IGFBP1, EGFR, and CDKN1C, suggesting that CTD-2218G20.2 might participate in the cancer progression via these cancer-related proteins. In summary, the systematic analysis of the prognostic lncRNAs and PCGs was of great importance to the understanding of the progression of stage III gastric cancer.https://www.frontiersin.org/article/10.3389/fgene.2020.00027/fullgastric cancerlong noncoding RNAprognosticTCGAmodel |
| spellingShingle | Xiaohui Su Jianjun Zhang Wei Yang Yanqing Liu Yang Liu Zexing Shan Wentao Wang Identification of the Prognosis-Related lncRNAs and Genes in Gastric Cancer Frontiers in Genetics gastric cancer long noncoding RNA prognostic TCGA model |
| title | Identification of the Prognosis-Related lncRNAs and Genes in Gastric Cancer |
| title_full | Identification of the Prognosis-Related lncRNAs and Genes in Gastric Cancer |
| title_fullStr | Identification of the Prognosis-Related lncRNAs and Genes in Gastric Cancer |
| title_full_unstemmed | Identification of the Prognosis-Related lncRNAs and Genes in Gastric Cancer |
| title_short | Identification of the Prognosis-Related lncRNAs and Genes in Gastric Cancer |
| title_sort | identification of the prognosis related lncrnas and genes in gastric cancer |
| topic | gastric cancer long noncoding RNA prognostic TCGA model |
| url | https://www.frontiersin.org/article/10.3389/fgene.2020.00027/full |
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