Pseudogenes and the associated ceRNA network as potential prognostic biomarkers for colorectal cancer
Abstract Colorectal cancer (CRC) is one of the most common and malignant carcinomas. Many long noncoding RNAs (lncRNAs) have been reported to play important roles in the tumorigenesis of CRC by influencing the expression of some mRNAs via competing endogenous RNA (ceRNA) networks and interacting wit...
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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/s41598-022-22768-y |
| _version_ | 1811250035657015296 |
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| author | Zhuoqi Li Jing Zhou Liankun Gu Baozhen Zhang |
| author_facet | Zhuoqi Li Jing Zhou Liankun Gu Baozhen Zhang |
| author_sort | Zhuoqi Li |
| collection | DOAJ |
| description | Abstract Colorectal cancer (CRC) is one of the most common and malignant carcinomas. Many long noncoding RNAs (lncRNAs) have been reported to play important roles in the tumorigenesis of CRC by influencing the expression of some mRNAs via competing endogenous RNA (ceRNA) networks and interacting with miRNAs. Pseudogene is one kind of lncRNA and can act as RNA sponges for miRNAs and regulate gene expression via ceRNA networks. However, there are few studies about pseudogenes in CRC. In this study, 31 differentially expressed (DE) pseudogenes, 17 DE miRNAs and 152 DE mRNAs were identified by analyzing the expression profiles of colon adenocarcinoma obtained from The Cancer Genome Atlas. A ceRNA network was constructed based on these RNAs. Kaplan–Meier analysis showed that 7 pseudogenes, 4 miRNAs and 30 mRNAs were significantly associated with overall survival. Then multivariate Cox regression analysis of the ceRNA-related DE pseudogenes was performed and a 5-pseudogene signature with the greatest prognostic value for CRC was identified. Moreover, the results were validated by the Gene Expression Omnibus database, and quantitative real-time PCR in 113 pairs of CRC tissues and colon cancer cell lines. This study provides a pseudogene-associated ceRNA network, 7 prognostic pseudogene biomarkers, and a 5-pseudogene prognostic risk signature that may be useful for predicting the survival of CRC patients. |
| first_indexed | 2024-04-12T15:58:08Z |
| format | Article |
| id | doaj.art-4fd458a8617c41b5830291e39cf40153 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-12T15:58:08Z |
| publishDate | 2022-10-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-4fd458a8617c41b5830291e39cf401532022-12-22T03:26:18ZengNature PortfolioScientific Reports2045-23222022-10-0112111110.1038/s41598-022-22768-yPseudogenes and the associated ceRNA network as potential prognostic biomarkers for colorectal cancerZhuoqi Li0Jing Zhou1Liankun Gu2Baozhen Zhang3Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and InstituteKey Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and InstituteKey Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and InstituteKey Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and InstituteAbstract Colorectal cancer (CRC) is one of the most common and malignant carcinomas. Many long noncoding RNAs (lncRNAs) have been reported to play important roles in the tumorigenesis of CRC by influencing the expression of some mRNAs via competing endogenous RNA (ceRNA) networks and interacting with miRNAs. Pseudogene is one kind of lncRNA and can act as RNA sponges for miRNAs and regulate gene expression via ceRNA networks. However, there are few studies about pseudogenes in CRC. In this study, 31 differentially expressed (DE) pseudogenes, 17 DE miRNAs and 152 DE mRNAs were identified by analyzing the expression profiles of colon adenocarcinoma obtained from The Cancer Genome Atlas. A ceRNA network was constructed based on these RNAs. Kaplan–Meier analysis showed that 7 pseudogenes, 4 miRNAs and 30 mRNAs were significantly associated with overall survival. Then multivariate Cox regression analysis of the ceRNA-related DE pseudogenes was performed and a 5-pseudogene signature with the greatest prognostic value for CRC was identified. Moreover, the results were validated by the Gene Expression Omnibus database, and quantitative real-time PCR in 113 pairs of CRC tissues and colon cancer cell lines. This study provides a pseudogene-associated ceRNA network, 7 prognostic pseudogene biomarkers, and a 5-pseudogene prognostic risk signature that may be useful for predicting the survival of CRC patients.https://doi.org/10.1038/s41598-022-22768-y |
| spellingShingle | Zhuoqi Li Jing Zhou Liankun Gu Baozhen Zhang Pseudogenes and the associated ceRNA network as potential prognostic biomarkers for colorectal cancer Scientific Reports |
| title | Pseudogenes and the associated ceRNA network as potential prognostic biomarkers for colorectal cancer |
| title_full | Pseudogenes and the associated ceRNA network as potential prognostic biomarkers for colorectal cancer |
| title_fullStr | Pseudogenes and the associated ceRNA network as potential prognostic biomarkers for colorectal cancer |
| title_full_unstemmed | Pseudogenes and the associated ceRNA network as potential prognostic biomarkers for colorectal cancer |
| title_short | Pseudogenes and the associated ceRNA network as potential prognostic biomarkers for colorectal cancer |
| title_sort | pseudogenes and the associated cerna network as potential prognostic biomarkers for colorectal cancer |
| url | https://doi.org/10.1038/s41598-022-22768-y |
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