Prognostic analysis of m6A-related lncRNAs as potential biomarkers in intrahepatic cholangiocarcinom
Intrahepatic cholangiocarcinoma (iCCA) patients had no obvious symptoms at early stage and poor postoperative survival. Therefore, the establishment of an iCCA prognostic prediction model to carry out refined management of iCCA patients is expected to improve the survival of the iCCA patient populat...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-09-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.982707/full |
| _version_ | 1798002184367898624 |
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| author | Guodong Shi Junjie Wang Weiqi Wang Min Chen Xiaoxuan Liu Yufan Zheng Yi Fu Minghua Wang Xiaojie Zhang |
| author_facet | Guodong Shi Junjie Wang Weiqi Wang Min Chen Xiaoxuan Liu Yufan Zheng Yi Fu Minghua Wang Xiaojie Zhang |
| author_sort | Guodong Shi |
| collection | DOAJ |
| description | Intrahepatic cholangiocarcinoma (iCCA) patients had no obvious symptoms at early stage and poor postoperative survival. Therefore, the establishment of an iCCA prognostic prediction model to carry out refined management of iCCA patients is expected to improve the survival of the iCCA patient population. In this paper, we analyzed the expression profiling data of patients from 32 iCCA tissues and eight paracancerous tissues in The Cancer Genome Atlas (TCGA) database. Perl software was used to separate M6A-related genes and lncRNAs from expression matrix files obtained from the TCGA database. The differentially expressed lncRNAs in the iCCA samples and the normal samples were screened out by differential analysis using the R package limma, and the m6A-related lncRNAs were further screened by Pearson correlation analysis. WGCNA clustering analysis constructs a random network to extract the module genes most related to iCCA, and take the intersection of differentially expressed lncRNAs related to m6A. Univariate Cox screening was performed for the intersection lncRNAs that had significant influence on the prognosis of iCCA patients, and further screening was performed by LASSO method and multivariate Cox regression analysis. Risk model was constructed and prognostic ability was evaluated according to risk score. In conclusion, we identified four m6A-related lncRNAs with potential prognostic value in iCCA, and established a novel m6A-related lncRNA-based prognostic model, which can be used as an independent prognostic factor to predict the prognosis of clinical patients. |
| first_indexed | 2024-04-11T11:49:04Z |
| format | Article |
| id | doaj.art-cb45991b8bfc48fbb4c53e5dad91dfa0 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-11T11:49:04Z |
| publishDate | 2022-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-cb45991b8bfc48fbb4c53e5dad91dfa02022-12-22T04:25:27ZengFrontiers Media S.A.Frontiers in Genetics1664-80212022-09-011310.3389/fgene.2022.982707982707Prognostic analysis of m6A-related lncRNAs as potential biomarkers in intrahepatic cholangiocarcinomGuodong Shi0Junjie Wang1Weiqi Wang2Min Chen3Xiaoxuan Liu4Yufan Zheng5Yi Fu6Minghua Wang7Xiaojie Zhang8Department of Biochemistry and Molecular Biology, Medical College, Soochow University, Suzhou, ChinaDepartment of Biochemistry and Molecular Biology, Medical College, Soochow University, Suzhou, ChinaDepartment of Biochemistry and Molecular Biology, Medical College, Soochow University, Suzhou, ChinaDepartment of Biochemistry and Molecular Biology, Medical College, Soochow University, Suzhou, ChinaDepartment of Biochemistry and Molecular Biology, Medical College, Soochow University, Suzhou, ChinaDepartment of Biochemistry and Molecular Biology, Medical College, Soochow University, Suzhou, ChinaDepartment of Human Anatomy, Histology and Embryology, Medical College, Soochow University, Suzhou, ChinaDepartment of Biochemistry and Molecular Biology, Medical College, Soochow University, Suzhou, ChinaDepartment of Experimental Center, Medical College, Soochow University, Suzhou, ChinaIntrahepatic cholangiocarcinoma (iCCA) patients had no obvious symptoms at early stage and poor postoperative survival. Therefore, the establishment of an iCCA prognostic prediction model to carry out refined management of iCCA patients is expected to improve the survival of the iCCA patient population. In this paper, we analyzed the expression profiling data of patients from 32 iCCA tissues and eight paracancerous tissues in The Cancer Genome Atlas (TCGA) database. Perl software was used to separate M6A-related genes and lncRNAs from expression matrix files obtained from the TCGA database. The differentially expressed lncRNAs in the iCCA samples and the normal samples were screened out by differential analysis using the R package limma, and the m6A-related lncRNAs were further screened by Pearson correlation analysis. WGCNA clustering analysis constructs a random network to extract the module genes most related to iCCA, and take the intersection of differentially expressed lncRNAs related to m6A. Univariate Cox screening was performed for the intersection lncRNAs that had significant influence on the prognosis of iCCA patients, and further screening was performed by LASSO method and multivariate Cox regression analysis. Risk model was constructed and prognostic ability was evaluated according to risk score. In conclusion, we identified four m6A-related lncRNAs with potential prognostic value in iCCA, and established a novel m6A-related lncRNA-based prognostic model, which can be used as an independent prognostic factor to predict the prognosis of clinical patients.https://www.frontiersin.org/articles/10.3389/fgene.2022.982707/fullintrahepatic cholangiocarcinomaN6-methyladenosinelong non-coding RNAgene co-expression networkprognostic signature |
| spellingShingle | Guodong Shi Junjie Wang Weiqi Wang Min Chen Xiaoxuan Liu Yufan Zheng Yi Fu Minghua Wang Xiaojie Zhang Prognostic analysis of m6A-related lncRNAs as potential biomarkers in intrahepatic cholangiocarcinom Frontiers in Genetics intrahepatic cholangiocarcinoma N6-methyladenosine long non-coding RNA gene co-expression network prognostic signature |
| title | Prognostic analysis of m6A-related lncRNAs as potential biomarkers in intrahepatic cholangiocarcinom |
| title_full | Prognostic analysis of m6A-related lncRNAs as potential biomarkers in intrahepatic cholangiocarcinom |
| title_fullStr | Prognostic analysis of m6A-related lncRNAs as potential biomarkers in intrahepatic cholangiocarcinom |
| title_full_unstemmed | Prognostic analysis of m6A-related lncRNAs as potential biomarkers in intrahepatic cholangiocarcinom |
| title_short | Prognostic analysis of m6A-related lncRNAs as potential biomarkers in intrahepatic cholangiocarcinom |
| title_sort | prognostic analysis of m6a related lncrnas as potential biomarkers in intrahepatic cholangiocarcinom |
| topic | intrahepatic cholangiocarcinoma N6-methyladenosine long non-coding RNA gene co-expression network prognostic signature |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.982707/full |
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