Signature construction and molecular subtype identification based on immune-related genes for better prediction of prognosis in hepatocellular carcinoma
Abstract Objective Hepatocellular carcinoma (HCC) immunotherapy is a focus of current research. We established a model that can effectively predict the prognosis and efficacy of HCC immunotherapy by analyzing the immune genes of HCC. Methods Through the data mining of hepatocellular carcinoma in The...
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| Format: | Article |
| Language: | English |
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BMC
2023-06-01
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| Series: | BMC Medical Genomics |
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| Online Access: | https://doi.org/10.1186/s12920-023-01558-z |
| _version_ | 1827922702649786368 |
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| author | Liang Sun Zhengyi Wu Cairong Dong Shian Yu He Huang Zhendong Chen Zhipeng Wu Xiangbao Yin |
| author_facet | Liang Sun Zhengyi Wu Cairong Dong Shian Yu He Huang Zhendong Chen Zhipeng Wu Xiangbao Yin |
| author_sort | Liang Sun |
| collection | DOAJ |
| description | Abstract Objective Hepatocellular carcinoma (HCC) immunotherapy is a focus of current research. We established a model that can effectively predict the prognosis and efficacy of HCC immunotherapy by analyzing the immune genes of HCC. Methods Through the data mining of hepatocellular carcinoma in The Cancer Genome Atlas (TCGA), the immune genes with differences in tumor and normal tissues are screened, and then the univariate regression analysis is carried out to screen the immune genes with differences related to prognosis. The prognosis model of immune related genes is constructed by using the minimum absolute contraction and selection operator (lasso) Cox regression model in the TCGA training set data, The risk score of each sample was calculated, and the survival was compared with the Kaplan Meier curve and the receiver operating characteristic (ROC) curve to evaluate the predictive ability. Data sets from ICGC and TCGA were used to verify the reliability of signatures. The correlation between clinicopathological features, immune infiltration, immune escape and risk score was analyzed. Results Seven immune genes were finally determined as the prognostic model of liver cancer. According to these 7 genes, the samples were divided into the high and low risk groups, and the results suggested that the high-risk group had a poorer prognosis, lower risk of immune escape, and better immunotherapy effect. In addition, the expression of TP53 and MSI was positively correlated in the high-risk group. Consensus clustering was performed to identify two main molecular subtypes (named clusters 1 and 2) based on the signature. It was found that compared with cluster 1, better survival outcome was observed in cluster 2. Conclusion Signature construction and molecular subtype identification of immune-related genes could be used to predict the prognosis of HCC, which may provide a specific reference for the development of novel biomarkers for HCC immunotherapy. |
| first_indexed | 2024-03-13T04:46:31Z |
| format | Article |
| id | doaj.art-73cfcf9b062d4926831c322bd92e9b9d |
| institution | Directory Open Access Journal |
| issn | 1755-8794 |
| language | English |
| last_indexed | 2024-03-13T04:46:31Z |
| publishDate | 2023-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Medical Genomics |
| spelling | doaj.art-73cfcf9b062d4926831c322bd92e9b9d2023-06-18T11:27:31ZengBMCBMC Medical Genomics1755-87942023-06-0116111910.1186/s12920-023-01558-zSignature construction and molecular subtype identification based on immune-related genes for better prediction of prognosis in hepatocellular carcinomaLiang Sun0Zhengyi Wu1Cairong Dong2Shian Yu3He Huang4Zhendong Chen5Zhipeng Wu6Xiangbao Yin7Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Nanchang UniversityDepartment of Hepatobiliary Surgery, the Second Affiliated Hospital of Nanchang UniversityDepartment of Hepatobiliary Surgery, the Second Affiliated Hospital of Nanchang UniversityDepartment of Hepatobiliary Surgery, the Second Affiliated Hospital of Nanchang UniversityDepartment of Hepatobiliary Surgery, the Second Affiliated Hospital of Nanchang UniversityDepartment of Hepatobiliary Surgery, the Second Affiliated Hospital of Nanchang UniversityDepartment of Hepatobiliary Surgery, the Second Affiliated Hospital of Nanchang UniversityDepartment of Hepatobiliary Surgery, the Second Affiliated Hospital of Nanchang UniversityAbstract Objective Hepatocellular carcinoma (HCC) immunotherapy is a focus of current research. We established a model that can effectively predict the prognosis and efficacy of HCC immunotherapy by analyzing the immune genes of HCC. Methods Through the data mining of hepatocellular carcinoma in The Cancer Genome Atlas (TCGA), the immune genes with differences in tumor and normal tissues are screened, and then the univariate regression analysis is carried out to screen the immune genes with differences related to prognosis. The prognosis model of immune related genes is constructed by using the minimum absolute contraction and selection operator (lasso) Cox regression model in the TCGA training set data, The risk score of each sample was calculated, and the survival was compared with the Kaplan Meier curve and the receiver operating characteristic (ROC) curve to evaluate the predictive ability. Data sets from ICGC and TCGA were used to verify the reliability of signatures. The correlation between clinicopathological features, immune infiltration, immune escape and risk score was analyzed. Results Seven immune genes were finally determined as the prognostic model of liver cancer. According to these 7 genes, the samples were divided into the high and low risk groups, and the results suggested that the high-risk group had a poorer prognosis, lower risk of immune escape, and better immunotherapy effect. In addition, the expression of TP53 and MSI was positively correlated in the high-risk group. Consensus clustering was performed to identify two main molecular subtypes (named clusters 1 and 2) based on the signature. It was found that compared with cluster 1, better survival outcome was observed in cluster 2. Conclusion Signature construction and molecular subtype identification of immune-related genes could be used to predict the prognosis of HCC, which may provide a specific reference for the development of novel biomarkers for HCC immunotherapy.https://doi.org/10.1186/s12920-023-01558-zHepatocellular carcinomaPrognostic modelBioinformaticsImmune microenvironmentImmunotherapy |
| spellingShingle | Liang Sun Zhengyi Wu Cairong Dong Shian Yu He Huang Zhendong Chen Zhipeng Wu Xiangbao Yin Signature construction and molecular subtype identification based on immune-related genes for better prediction of prognosis in hepatocellular carcinoma BMC Medical Genomics Hepatocellular carcinoma Prognostic model Bioinformatics Immune microenvironment Immunotherapy |
| title | Signature construction and molecular subtype identification based on immune-related genes for better prediction of prognosis in hepatocellular carcinoma |
| title_full | Signature construction and molecular subtype identification based on immune-related genes for better prediction of prognosis in hepatocellular carcinoma |
| title_fullStr | Signature construction and molecular subtype identification based on immune-related genes for better prediction of prognosis in hepatocellular carcinoma |
| title_full_unstemmed | Signature construction and molecular subtype identification based on immune-related genes for better prediction of prognosis in hepatocellular carcinoma |
| title_short | Signature construction and molecular subtype identification based on immune-related genes for better prediction of prognosis in hepatocellular carcinoma |
| title_sort | signature construction and molecular subtype identification based on immune related genes for better prediction of prognosis in hepatocellular carcinoma |
| topic | Hepatocellular carcinoma Prognostic model Bioinformatics Immune microenvironment Immunotherapy |
| url | https://doi.org/10.1186/s12920-023-01558-z |
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