Integrating bulk and single-cell RNA sequencing data to establish necroptosis-related lncRNA risk model and analyze the immune microenvironment in hepatocellular carcinoma
Background: The increasing evidence suggests that necroptosis mediates many behaviors of tumors, as well as the regulation of the tumor microenvironment. Long non-coding RNAs (lncRNAs) are involved in a variety of regulatory processes during tumor development and are significantly associated with pa...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-11-01
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| Series: | Heliyon |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2405844023092915 |
| _version_ | 1797429731648339968 |
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| author | Rongjie Zhang Qian Li Xiaoxiao Yu Yiwen Hou Liang Yan Yating Gao Longshan Ji Xin Zhang Miao Fang Lingying Huang Zhuo Yu Yueqiu Gao Man Li |
| author_facet | Rongjie Zhang Qian Li Xiaoxiao Yu Yiwen Hou Liang Yan Yating Gao Longshan Ji Xin Zhang Miao Fang Lingying Huang Zhuo Yu Yueqiu Gao Man Li |
| author_sort | Rongjie Zhang |
| collection | DOAJ |
| description | Background: The increasing evidence suggests that necroptosis mediates many behaviors of tumors, as well as the regulation of the tumor microenvironment. Long non-coding RNAs (lncRNAs) are involved in a variety of regulatory processes during tumor development and are significantly associated with patient prognosis. It suggests that necroptosis-related lncRNAs (NRlncRNAs) may serve as biomarkers for the prognosis of hepatocellular carcinoma (HCC). Methods: lncRNA expression profiles of HCC were obtained from TCGA database. LncRNAs associated with necroptosis were extracted using correlation analysis. Prognostic models were constructed based on least absolute shrinkage and selection operator algorithm (LASSO) and multivariate Cox regression analysis. The differences of tumor microenvironment between high-risk and low-risk groups were further analyzed. Single-cell RNA sequencing data of HCC was performed to assess the enrichment of necroptosis-related genes in immune cell subsets. Finally, real-time RT-PCR was used to detect the prognosis-related lncRNAs expression in different HCC cell lines. Results: We constructed a prognostic signature based on 8 NRlncRNAs, which also showed good predictive accuracy. The model showed that the prognosis of patients with high-risk score was significantly worse than that of patients with low-risk score (P < 0.05). Combined with the clinical characteristics and risk score of HCC, Nomogram was drawn for reference in clinical practice. In addition, immune cell infiltration analysis and single cell RNA sequencing analysis showed that a low level of immune infiltration was observed in patients at high risk and that there was a significant correlation between NRlncRNAs and macrophages. The results of RT-qPCR also showed that 8 necroptosis-related lncRNAs were highly expressed in HCC cell lines and human liver cancer tissues. Conclusion: This prognostic signature based on the necroptosis-related lncRNAs may provide meaningful clinical insights for the prognosis and immunotherapy responses in patients with HCC. |
| first_indexed | 2024-03-09T09:17:23Z |
| format | Article |
| id | doaj.art-fb279ae1ed3d41f4ad313cfc6eb66e78 |
| institution | Directory Open Access Journal |
| issn | 2405-8440 |
| language | English |
| last_indexed | 2024-03-09T09:17:23Z |
| publishDate | 2023-11-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Heliyon |
| spelling | doaj.art-fb279ae1ed3d41f4ad313cfc6eb66e782023-12-02T07:05:07ZengElsevierHeliyon2405-84402023-11-01911e22083Integrating bulk and single-cell RNA sequencing data to establish necroptosis-related lncRNA risk model and analyze the immune microenvironment in hepatocellular carcinomaRongjie Zhang0Qian Li1Xiaoxiao Yu2Yiwen Hou3Liang Yan4Yating Gao5Longshan Ji6Xin Zhang7Miao Fang8Lingying Huang9Zhuo Yu10Yueqiu Gao11Man Li12Laboratory of cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, ChinaLaboratory of cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, ChinaLaboratory of cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, ChinaLaboratory of cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, ChinaGeneral Surgery Department of Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, ChinaLaboratory of cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, ChinaLaboratory of cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, ChinaLaboratory of cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, ChinaLaboratory of cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, ChinaDepartment of Hepatopathy, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, ChinaDepartment of Hepatopathy, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, ChinaLaboratory of cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, China; Institute of Infectious Diseases of Integrated Traditional Chinese and Western Medicine, China; Corresponding author. Laboratory of Cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, China.Laboratory of cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, China; Corresponding author.Background: The increasing evidence suggests that necroptosis mediates many behaviors of tumors, as well as the regulation of the tumor microenvironment. Long non-coding RNAs (lncRNAs) are involved in a variety of regulatory processes during tumor development and are significantly associated with patient prognosis. It suggests that necroptosis-related lncRNAs (NRlncRNAs) may serve as biomarkers for the prognosis of hepatocellular carcinoma (HCC). Methods: lncRNA expression profiles of HCC were obtained from TCGA database. LncRNAs associated with necroptosis were extracted using correlation analysis. Prognostic models were constructed based on least absolute shrinkage and selection operator algorithm (LASSO) and multivariate Cox regression analysis. The differences of tumor microenvironment between high-risk and low-risk groups were further analyzed. Single-cell RNA sequencing data of HCC was performed to assess the enrichment of necroptosis-related genes in immune cell subsets. Finally, real-time RT-PCR was used to detect the prognosis-related lncRNAs expression in different HCC cell lines. Results: We constructed a prognostic signature based on 8 NRlncRNAs, which also showed good predictive accuracy. The model showed that the prognosis of patients with high-risk score was significantly worse than that of patients with low-risk score (P < 0.05). Combined with the clinical characteristics and risk score of HCC, Nomogram was drawn for reference in clinical practice. In addition, immune cell infiltration analysis and single cell RNA sequencing analysis showed that a low level of immune infiltration was observed in patients at high risk and that there was a significant correlation between NRlncRNAs and macrophages. The results of RT-qPCR also showed that 8 necroptosis-related lncRNAs were highly expressed in HCC cell lines and human liver cancer tissues. Conclusion: This prognostic signature based on the necroptosis-related lncRNAs may provide meaningful clinical insights for the prognosis and immunotherapy responses in patients with HCC.http://www.sciencedirect.com/science/article/pii/S2405844023092915Hepatocellular carcinomalncRNANecroptosisPrognosis |
| spellingShingle | Rongjie Zhang Qian Li Xiaoxiao Yu Yiwen Hou Liang Yan Yating Gao Longshan Ji Xin Zhang Miao Fang Lingying Huang Zhuo Yu Yueqiu Gao Man Li Integrating bulk and single-cell RNA sequencing data to establish necroptosis-related lncRNA risk model and analyze the immune microenvironment in hepatocellular carcinoma Heliyon Hepatocellular carcinoma lncRNA Necroptosis Prognosis |
| title | Integrating bulk and single-cell RNA sequencing data to establish necroptosis-related lncRNA risk model and analyze the immune microenvironment in hepatocellular carcinoma |
| title_full | Integrating bulk and single-cell RNA sequencing data to establish necroptosis-related lncRNA risk model and analyze the immune microenvironment in hepatocellular carcinoma |
| title_fullStr | Integrating bulk and single-cell RNA sequencing data to establish necroptosis-related lncRNA risk model and analyze the immune microenvironment in hepatocellular carcinoma |
| title_full_unstemmed | Integrating bulk and single-cell RNA sequencing data to establish necroptosis-related lncRNA risk model and analyze the immune microenvironment in hepatocellular carcinoma |
| title_short | Integrating bulk and single-cell RNA sequencing data to establish necroptosis-related lncRNA risk model and analyze the immune microenvironment in hepatocellular carcinoma |
| title_sort | integrating bulk and single cell rna sequencing data to establish necroptosis related lncrna risk model and analyze the immune microenvironment in hepatocellular carcinoma |
| topic | Hepatocellular carcinoma lncRNA Necroptosis Prognosis |
| url | http://www.sciencedirect.com/science/article/pii/S2405844023092915 |
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