Prognosis-Related Molecular Subtypes and Immune Features Associated with Hepatocellular Carcinoma
Bioinformatics tools were used to identify prognosis-related molecular subtypes and biomarkers of hepatocellular carcinoma (HCC). Differential expression analysis of four datasets identified 3330 overlapping differentially expressed genes (DEGs) in the same direction in all four datasets. Those gene...
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MDPI AG
2022-11-01
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| Series: | Cancers |
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| Online Access: | https://www.mdpi.com/2072-6694/14/22/5721 |
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| author | Jiazhou Ye Yan Lin Xing Gao Lu Lu Xi Huang Shilin Huang Tao Bai Guobin Wu Xiaoling Luo Yongqiang Li Rong Liang |
| author_facet | Jiazhou Ye Yan Lin Xing Gao Lu Lu Xi Huang Shilin Huang Tao Bai Guobin Wu Xiaoling Luo Yongqiang Li Rong Liang |
| author_sort | Jiazhou Ye |
| collection | DOAJ |
| description | Bioinformatics tools were used to identify prognosis-related molecular subtypes and biomarkers of hepatocellular carcinoma (HCC). Differential expression analysis of four datasets identified 3330 overlapping differentially expressed genes (DEGs) in the same direction in all four datasets. Those genes were involved in the cell cycle, FOXO signaling pathway, as well as complement and coagulation cascades. Based on non-negative matrix decomposition, two molecular subtypes of HCC with different prognoses were identified, with subtype C2 showing better overall survival than subtype C1. Cox regression and Kaplan-Meier analysis showed that 217 of the overlapping DEGs were closely associated with HCC prognosis. The subset of those genes showing an area under the curve >0.80 was used to construct random survival forest and least absolute shrinkage and selection operator models, which identified seven feature genes (SORBS2, DHRS1, SLC16A2, RCL1, IGFALS, GNA14, and FANCI) that may be involved in HCC occurrence and prognosis. Based on the feature genes, risk score and recurrence models were constructed, while a univariate Cox model identified FANCI as a key gene involved mainly in the cell cycle, DNA replication, and mismatch repair. Further analysis showed that FANCI had two mutation sites and that its gene may undergo methylation. Single-sample gene set enrichment analysis showed that Th2 and T helper cells are significantly upregulated in HCC patients compared to controls. Our results identify FANCI as a potential prognostic biomarker for HCC. |
| first_indexed | 2024-03-09T18:25:48Z |
| format | Article |
| id | doaj.art-d55c1bd3b476484d97acb7030177408d |
| institution | Directory Open Access Journal |
| issn | 2072-6694 |
| language | English |
| last_indexed | 2024-03-09T18:25:48Z |
| publishDate | 2022-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cancers |
| spelling | doaj.art-d55c1bd3b476484d97acb7030177408d2023-11-24T07:55:38ZengMDPI AGCancers2072-66942022-11-011422572110.3390/cancers14225721Prognosis-Related Molecular Subtypes and Immune Features Associated with Hepatocellular CarcinomaJiazhou Ye0Yan Lin1Xing Gao2Lu Lu3Xi Huang4Shilin Huang5Tao Bai6Guobin Wu7Xiaoling Luo8Yongqiang Li9Rong Liang10Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, ChinaDepartment of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning 530021, ChinaDepartment of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning 530021, ChinaDepartment of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning 530021, ChinaDepartment of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning 530021, ChinaDepartment of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning 530021, ChinaDepartment of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, ChinaDepartment of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, ChinaDepartment of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning 530021, ChinaDepartment of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning 530021, ChinaDepartment of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning 530021, ChinaBioinformatics tools were used to identify prognosis-related molecular subtypes and biomarkers of hepatocellular carcinoma (HCC). Differential expression analysis of four datasets identified 3330 overlapping differentially expressed genes (DEGs) in the same direction in all four datasets. Those genes were involved in the cell cycle, FOXO signaling pathway, as well as complement and coagulation cascades. Based on non-negative matrix decomposition, two molecular subtypes of HCC with different prognoses were identified, with subtype C2 showing better overall survival than subtype C1. Cox regression and Kaplan-Meier analysis showed that 217 of the overlapping DEGs were closely associated with HCC prognosis. The subset of those genes showing an area under the curve >0.80 was used to construct random survival forest and least absolute shrinkage and selection operator models, which identified seven feature genes (SORBS2, DHRS1, SLC16A2, RCL1, IGFALS, GNA14, and FANCI) that may be involved in HCC occurrence and prognosis. Based on the feature genes, risk score and recurrence models were constructed, while a univariate Cox model identified FANCI as a key gene involved mainly in the cell cycle, DNA replication, and mismatch repair. Further analysis showed that FANCI had two mutation sites and that its gene may undergo methylation. Single-sample gene set enrichment analysis showed that Th2 and T helper cells are significantly upregulated in HCC patients compared to controls. Our results identify FANCI as a potential prognostic biomarker for HCC.https://www.mdpi.com/2072-6694/14/22/5721hepatocellular carcinomamolecular subtypesbioinformaticsFANCIprognostic biomarker |
| spellingShingle | Jiazhou Ye Yan Lin Xing Gao Lu Lu Xi Huang Shilin Huang Tao Bai Guobin Wu Xiaoling Luo Yongqiang Li Rong Liang Prognosis-Related Molecular Subtypes and Immune Features Associated with Hepatocellular Carcinoma Cancers hepatocellular carcinoma molecular subtypes bioinformatics FANCI prognostic biomarker |
| title | Prognosis-Related Molecular Subtypes and Immune Features Associated with Hepatocellular Carcinoma |
| title_full | Prognosis-Related Molecular Subtypes and Immune Features Associated with Hepatocellular Carcinoma |
| title_fullStr | Prognosis-Related Molecular Subtypes and Immune Features Associated with Hepatocellular Carcinoma |
| title_full_unstemmed | Prognosis-Related Molecular Subtypes and Immune Features Associated with Hepatocellular Carcinoma |
| title_short | Prognosis-Related Molecular Subtypes and Immune Features Associated with Hepatocellular Carcinoma |
| title_sort | prognosis related molecular subtypes and immune features associated with hepatocellular carcinoma |
| topic | hepatocellular carcinoma molecular subtypes bioinformatics FANCI prognostic biomarker |
| url | https://www.mdpi.com/2072-6694/14/22/5721 |
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