Potential mechanisms and prognostic model of eRNAs-regulated genes in stomach adenocarcinoma
Abstract Gastric Carcinoma is the fourth leading cause of cancer deaths worldwide, in which stomach adenocarcinoma (STAD) is the most common histological type. A growing amount of evidence has suggested the importance of enhancer RNAs (eRNAs) in the cancer. However, the potential mechanism of eRNAs...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2022-10-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-022-20824-1 |
| _version_ | 1811194915033448448 |
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| author | Liuying Gao Hao Rong |
| author_facet | Liuying Gao Hao Rong |
| author_sort | Liuying Gao |
| collection | DOAJ |
| description | Abstract Gastric Carcinoma is the fourth leading cause of cancer deaths worldwide, in which stomach adenocarcinoma (STAD) is the most common histological type. A growing amount of evidence has suggested the importance of enhancer RNAs (eRNAs) in the cancer. However, the potential mechanism of eRNAs in STAD remains unclear. The eRNAs-regulated genes (eRRGs) were identified through four different enhancer resources. The differentially expressed eRRGs were obtained by ‘DESeq2’ R package. The prognosis prediction model was constructed by Cox and Lasso regression analysis. The ‘ChAMP’ R package and ‘maftools’ R package were used to investigate the multi-omics characters. In this study, combining the concept of contact domain, a total of 9014 eRRGs including 4926 PCGs and 4088 lncRNAs were identified and these eRRGs showed higher and more stable expression. Besides, the functions of these genes were mainly associated with tumor-related biological processes. Then, a prognostic prediction model was constructed and the AUC values of the 1-, 3- and 5-year survival prediction reached 0.76, 0.84 and 0.84, respectively, indicating that this model has a high accuracy. Finally, the difference between high-risk group and low-risk group were investigated using multi-omics data including gene expression, DNA methylation and somatic mutations. Our study provides significant clues for the elucidation of eRNAs in STAD and may help improve the overall survival for STAD patients. |
| first_indexed | 2024-04-12T00:35:15Z |
| format | Article |
| id | doaj.art-71c176a84796483cb21e6efd9cb04395 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-12T00:35:15Z |
| publishDate | 2022-10-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-71c176a84796483cb21e6efd9cb043952022-12-22T03:55:11ZengNature PortfolioScientific Reports2045-23222022-10-0112111310.1038/s41598-022-20824-1Potential mechanisms and prognostic model of eRNAs-regulated genes in stomach adenocarcinomaLiuying Gao0Hao Rong1The Affiliated People’s Hospital of Ningbo UniversityThe Affiliated People’s Hospital of Ningbo UniversityAbstract Gastric Carcinoma is the fourth leading cause of cancer deaths worldwide, in which stomach adenocarcinoma (STAD) is the most common histological type. A growing amount of evidence has suggested the importance of enhancer RNAs (eRNAs) in the cancer. However, the potential mechanism of eRNAs in STAD remains unclear. The eRNAs-regulated genes (eRRGs) were identified through four different enhancer resources. The differentially expressed eRRGs were obtained by ‘DESeq2’ R package. The prognosis prediction model was constructed by Cox and Lasso regression analysis. The ‘ChAMP’ R package and ‘maftools’ R package were used to investigate the multi-omics characters. In this study, combining the concept of contact domain, a total of 9014 eRRGs including 4926 PCGs and 4088 lncRNAs were identified and these eRRGs showed higher and more stable expression. Besides, the functions of these genes were mainly associated with tumor-related biological processes. Then, a prognostic prediction model was constructed and the AUC values of the 1-, 3- and 5-year survival prediction reached 0.76, 0.84 and 0.84, respectively, indicating that this model has a high accuracy. Finally, the difference between high-risk group and low-risk group were investigated using multi-omics data including gene expression, DNA methylation and somatic mutations. Our study provides significant clues for the elucidation of eRNAs in STAD and may help improve the overall survival for STAD patients.https://doi.org/10.1038/s41598-022-20824-1 |
| spellingShingle | Liuying Gao Hao Rong Potential mechanisms and prognostic model of eRNAs-regulated genes in stomach adenocarcinoma Scientific Reports |
| title | Potential mechanisms and prognostic model of eRNAs-regulated genes in stomach adenocarcinoma |
| title_full | Potential mechanisms and prognostic model of eRNAs-regulated genes in stomach adenocarcinoma |
| title_fullStr | Potential mechanisms and prognostic model of eRNAs-regulated genes in stomach adenocarcinoma |
| title_full_unstemmed | Potential mechanisms and prognostic model of eRNAs-regulated genes in stomach adenocarcinoma |
| title_short | Potential mechanisms and prognostic model of eRNAs-regulated genes in stomach adenocarcinoma |
| title_sort | potential mechanisms and prognostic model of ernas regulated genes in stomach adenocarcinoma |
| url | https://doi.org/10.1038/s41598-022-20824-1 |
| work_keys_str_mv | AT liuyinggao potentialmechanismsandprognosticmodelofernasregulatedgenesinstomachadenocarcinoma AT haorong potentialmechanismsandprognosticmodelofernasregulatedgenesinstomachadenocarcinoma |