Development of a prognostic gene signature for hepatocellular carcinoma
Accurate prediction of overall survival is important for prognosis and the assignment of appropriate personalized clinical treatment in hepatocellular carcinoma (HCC) patients. The aim of the present study was to establish an optimal gene model for the independent prediction of prognosis associated...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-01-01
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| Series: | Cancer Treatment and Research Communications |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S246829422200003X |
| _version_ | 1818201220862443520 |
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| author | Cuiyun Wu Yaosheng Luo Yinghui Chen Hongling Qu Lin Zheng Jie Yao |
| author_facet | Cuiyun Wu Yaosheng Luo Yinghui Chen Hongling Qu Lin Zheng Jie Yao |
| author_sort | Cuiyun Wu |
| collection | DOAJ |
| description | Accurate prediction of overall survival is important for prognosis and the assignment of appropriate personalized clinical treatment in hepatocellular carcinoma (HCC) patients. The aim of the present study was to establish an optimal gene model for the independent prediction of prognosis associated with common clinical patterns. Gene expression profiles and the corresponding clinical information of the LIHC cohort were obtained from The Cancer Genome Atlas. Differentially expressed genes were found using the R package “limma”. Subsequently, a prognostic gene signature was developed using the LASSO Cox regression model. Kaplan–Meier, log-rank, and receiver operating characteristic (ROC) analyses were performed to verify the predictive accuracy of the prognostic model. Finally, a nomogram and calibration plot were created using the “rms” package. Differentially expressed genes were screened with threshold criteria (FDR < 0.01 and |log FC|>3) and 563 differentially expressed genes were obtained, including 448 downregulated and 115 upregulated genes. Using the LASSO Cox regression model, a prognostic gene signature was developed based on nine genes, IQGAP3, BIRC5, PTTG1, STC2, CDKN3, PBK, EXO1, NEIL3, and HOXD9, the expression levels of which were quantitated using RT-qPCR. According to the risk scores, patients were separated into high-risk and low-risk groups. In conclusion, the prognostic gene signature can be used as a combined biomarker for the independent prediction of overall survival in HCC patients. Moreover, we created a nomogram that can be used to infer prognosis and aid individualized decisions regarding treatment and surveillance. |
| first_indexed | 2024-12-12T02:50:06Z |
| format | Article |
| id | doaj.art-ab6186eaead44540abcf30f39cb7dadb |
| institution | Directory Open Access Journal |
| issn | 2468-2942 |
| language | English |
| last_indexed | 2024-12-12T02:50:06Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Cancer Treatment and Research Communications |
| spelling | doaj.art-ab6186eaead44540abcf30f39cb7dadb2022-12-22T00:40:55ZengElsevierCancer Treatment and Research Communications2468-29422022-01-0131100511Development of a prognostic gene signature for hepatocellular carcinomaCuiyun Wu0Yaosheng Luo1Yinghui Chen2Hongling Qu3Lin Zheng4Jie Yao5Department of Laboratory, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, 528308, Guangdong, ChinaMedical research center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, 528308, Guangdong, ChinaDepartment of Laboratory, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, 528308, Guangdong, ChinaDepartment of Laboratory, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, 528308, Guangdong, ChinaDepartment of Laboratory, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, 528308, Guangdong, ChinaDepartment of Laboratory, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, 528308, Guangdong, China; Medical research center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, 528308, Guangdong, China; Corresponding author at: Shunde Hospital, Southern Medical University, Foshan, Guangdong, China. 528308.Accurate prediction of overall survival is important for prognosis and the assignment of appropriate personalized clinical treatment in hepatocellular carcinoma (HCC) patients. The aim of the present study was to establish an optimal gene model for the independent prediction of prognosis associated with common clinical patterns. Gene expression profiles and the corresponding clinical information of the LIHC cohort were obtained from The Cancer Genome Atlas. Differentially expressed genes were found using the R package “limma”. Subsequently, a prognostic gene signature was developed using the LASSO Cox regression model. Kaplan–Meier, log-rank, and receiver operating characteristic (ROC) analyses were performed to verify the predictive accuracy of the prognostic model. Finally, a nomogram and calibration plot were created using the “rms” package. Differentially expressed genes were screened with threshold criteria (FDR < 0.01 and |log FC|>3) and 563 differentially expressed genes were obtained, including 448 downregulated and 115 upregulated genes. Using the LASSO Cox regression model, a prognostic gene signature was developed based on nine genes, IQGAP3, BIRC5, PTTG1, STC2, CDKN3, PBK, EXO1, NEIL3, and HOXD9, the expression levels of which were quantitated using RT-qPCR. According to the risk scores, patients were separated into high-risk and low-risk groups. In conclusion, the prognostic gene signature can be used as a combined biomarker for the independent prediction of overall survival in HCC patients. Moreover, we created a nomogram that can be used to infer prognosis and aid individualized decisions regarding treatment and surveillance.http://www.sciencedirect.com/science/article/pii/S246829422200003XHepatocellular carcinomaDifferentially expressed genePrognostic gene signature |
| spellingShingle | Cuiyun Wu Yaosheng Luo Yinghui Chen Hongling Qu Lin Zheng Jie Yao Development of a prognostic gene signature for hepatocellular carcinoma Cancer Treatment and Research Communications Hepatocellular carcinoma Differentially expressed gene Prognostic gene signature |
| title | Development of a prognostic gene signature for hepatocellular carcinoma |
| title_full | Development of a prognostic gene signature for hepatocellular carcinoma |
| title_fullStr | Development of a prognostic gene signature for hepatocellular carcinoma |
| title_full_unstemmed | Development of a prognostic gene signature for hepatocellular carcinoma |
| title_short | Development of a prognostic gene signature for hepatocellular carcinoma |
| title_sort | development of a prognostic gene signature for hepatocellular carcinoma |
| topic | Hepatocellular carcinoma Differentially expressed gene Prognostic gene signature |
| url | http://www.sciencedirect.com/science/article/pii/S246829422200003X |
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