Identification of DNA repair gene signature and potential molecular subtypes in hepatocellular carcinoma
DNA repair is a critical factor in tumor progression as it impacts tumor mutational burden, genome stability, PD-L1 expression, immunotherapy response, and tumor-infiltrating lymphocytes (TILs). In this study, we present a prognostic model for hepatocellular carcinoma (HCC) that utilizes genes relat...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-05-01
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| Series: | Frontiers in Oncology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fonc.2023.1180722/full |
| _version_ | 1797826302316642304 |
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| author | Yi Bai Jinyun He Yanquan Ma He Liang Ming Li Yan Wu |
| author_facet | Yi Bai Jinyun He Yanquan Ma He Liang Ming Li Yan Wu |
| author_sort | Yi Bai |
| collection | DOAJ |
| description | DNA repair is a critical factor in tumor progression as it impacts tumor mutational burden, genome stability, PD-L1 expression, immunotherapy response, and tumor-infiltrating lymphocytes (TILs). In this study, we present a prognostic model for hepatocellular carcinoma (HCC) that utilizes genes related to the DNA damage response (DDR). Patients were stratified based on their risk score, and groups with lower risk scores demonstrated better survival rates compared to those with higher risk scores. The prognostic model’s accuracy in predicting 1-, 3-, and 5-year survival rates for HCC patients was analyzed using receiver operator curve analysis (ROC). Results showed good accuracy in predicting survival rates. Additionally, we evaluated the prognostic model’s potential as an independent factor for HCC prognosis, along with tumor stage. Furthermore, nomogram was employed to determine the overall survival year of patients with HCC based on this independent factor. Gene set enrichment analysis (GSEA) revealed that in the high-risk group, apoptosis, cell cycle, MAPK, mTOR, and WNT cascades were highly enriched. We used training and validation datasets to identify potential molecular subtypes of HCC based on the expression of DDR genes. The two subtypes differed in terms of checkpoint receptors for immunity and immune cell filtration capacity.Collectively, our study identified potential biomarkers of HCC prognosis, providing novel insights into the molecular mechanisms underlying HCC. |
| first_indexed | 2024-03-13T11:06:46Z |
| format | Article |
| id | doaj.art-b14a39ef805a42bbb0b90f2ff83a52e2 |
| institution | Directory Open Access Journal |
| issn | 2234-943X |
| language | English |
| last_indexed | 2024-03-13T11:06:46Z |
| publishDate | 2023-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Oncology |
| spelling | doaj.art-b14a39ef805a42bbb0b90f2ff83a52e22023-05-16T05:41:13ZengFrontiers Media S.A.Frontiers in Oncology2234-943X2023-05-011310.3389/fonc.2023.11807221180722Identification of DNA repair gene signature and potential molecular subtypes in hepatocellular carcinomaYi Bai0Jinyun He1Yanquan Ma2He Liang3Ming Li4Yan Wu5Department of Critical Care Medicine, Panjin Liaoyou Baoshihua Hospital, Liaoning, ChinaDepartment of hepatobiliary surgery, Panjin Liaoyou Baoshihua Hospital, Liaoning, ChinaDepartment of Critical Care Medicine, Panjin Liaoyou Baoshihua Hospital, Liaoning, ChinaDepartment of integrated Chinese and Western medicine, Panjin Liaoyou Baoshihua Hospital, Liaoning, ChinaFuxin Municipal Discipline Inspection Commission, Liaoning, ChinaDepartment of rheumatology and immunology, Panjin Liaoyou Baoshihua Hospital, Liaoning, ChinaDNA repair is a critical factor in tumor progression as it impacts tumor mutational burden, genome stability, PD-L1 expression, immunotherapy response, and tumor-infiltrating lymphocytes (TILs). In this study, we present a prognostic model for hepatocellular carcinoma (HCC) that utilizes genes related to the DNA damage response (DDR). Patients were stratified based on their risk score, and groups with lower risk scores demonstrated better survival rates compared to those with higher risk scores. The prognostic model’s accuracy in predicting 1-, 3-, and 5-year survival rates for HCC patients was analyzed using receiver operator curve analysis (ROC). Results showed good accuracy in predicting survival rates. Additionally, we evaluated the prognostic model’s potential as an independent factor for HCC prognosis, along with tumor stage. Furthermore, nomogram was employed to determine the overall survival year of patients with HCC based on this independent factor. Gene set enrichment analysis (GSEA) revealed that in the high-risk group, apoptosis, cell cycle, MAPK, mTOR, and WNT cascades were highly enriched. We used training and validation datasets to identify potential molecular subtypes of HCC based on the expression of DDR genes. The two subtypes differed in terms of checkpoint receptors for immunity and immune cell filtration capacity.Collectively, our study identified potential biomarkers of HCC prognosis, providing novel insights into the molecular mechanisms underlying HCC.https://www.frontiersin.org/articles/10.3389/fonc.2023.1180722/fullhepatocellular carcinomaDNA repair geneprognosismolecular subtypes of HCCimmune infiltrition |
| spellingShingle | Yi Bai Jinyun He Yanquan Ma He Liang Ming Li Yan Wu Identification of DNA repair gene signature and potential molecular subtypes in hepatocellular carcinoma Frontiers in Oncology hepatocellular carcinoma DNA repair gene prognosis molecular subtypes of HCC immune infiltrition |
| title | Identification of DNA repair gene signature and potential molecular subtypes in hepatocellular carcinoma |
| title_full | Identification of DNA repair gene signature and potential molecular subtypes in hepatocellular carcinoma |
| title_fullStr | Identification of DNA repair gene signature and potential molecular subtypes in hepatocellular carcinoma |
| title_full_unstemmed | Identification of DNA repair gene signature and potential molecular subtypes in hepatocellular carcinoma |
| title_short | Identification of DNA repair gene signature and potential molecular subtypes in hepatocellular carcinoma |
| title_sort | identification of dna repair gene signature and potential molecular subtypes in hepatocellular carcinoma |
| topic | hepatocellular carcinoma DNA repair gene prognosis molecular subtypes of HCC immune infiltrition |
| url | https://www.frontiersin.org/articles/10.3389/fonc.2023.1180722/full |
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