An 8-gene predicting survival model of hepatocellular carcinoma (HCC) related to pyroptosis and cuproptosis
Abstract Background The study aimed to establish a prognostic survival model with 8 pyroptosis-and-cuproptosis-related genes to examine the prognostic effect in patients of hepatocellular carcinoma (HCC). Methods We downloaded gene expression data and clinical information of HCC patients from The Ca...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-07-01
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| Series: | Hereditas |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s41065-023-00288-7 |
| _version_ | 1797774140171616256 |
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| author | Hongjin Wang Nian Wang Ze Tang Qiuyu Liu Shiyu Nie Wu Tao |
| author_facet | Hongjin Wang Nian Wang Ze Tang Qiuyu Liu Shiyu Nie Wu Tao |
| author_sort | Hongjin Wang |
| collection | DOAJ |
| description | Abstract Background The study aimed to establish a prognostic survival model with 8 pyroptosis-and-cuproptosis-related genes to examine the prognostic effect in patients of hepatocellular carcinoma (HCC). Methods We downloaded gene expression data and clinical information of HCC patients from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO). The clustering analysis and cox regression with LASSO were used for constructing an 8 PCmRNAs survival model. Using TCGA, ICGC and GEO cohort, the overall survival (OS) between high- and low- risk group was determined. We also evaluated independent prognostic indicators using univariate and multivariate analyses. The relatively bioinformatics analysis, including immune cell infiltration, function enrichment and drug sensitivity analyses, was performed as well. The gene expression of 8 PCmRNAs in vitro were validated in several HCC cell lines by qRT-PCR and Western blot. The relationship between GZMA and Fludarabine were further checked by CCK-8 assay. Results The survival prognostic model was constructed with ATP7A, GLS, CDKN2A, BAK1, CHMP4B, NLRP6, NOD1 and GZMA using data from TCGA cohort. The ICGC and GEO cohort were used for model validation. Receiver operating characteristic (ROC) curves showed a good survival prediction by this model. Risk scores had the highest predictable value for survival among Stage, Age, Gender and Grade. Most Immune cells and immune functions were decreased in high-risk group. Besides, function enrichment analyses showed that steroid metabolic process, hormone metabolic process, collagen − containing extracellular matrix, oxidoreductase activity and pyruvate metabolism were enriched. Potential drugs targeted different PCDEGs like Nelarabine, Dexamethasone and Fludarabine were found as well. ATP7A, GLS, CDKN2A, BAK1, CHMP4B, NOD1 were upregulated while NLRP6 and GZMA were downregulated in most HCC cell lines. The potential therapy of Fludarabine was demonstrated when GZMA was low expressed in Huh7 cell line. Conclusion We constructed a novel 8-gene (ATP7A, GLS, CDKN2A, BAK1, CHMP4B, NLRP6, NOD1 and GZMA) prognostic model and explored potential functional information and microenvironment of HCC, which might be worthy of clinical application. In addition, several potential chemotherapy drugs were screened and Fludarabine might be effective for HCC patients whose GZMA was low expressed. |
| first_indexed | 2024-03-12T22:16:38Z |
| format | Article |
| id | doaj.art-32cdbdd5da694115a04d9be5fcb8e769 |
| institution | Directory Open Access Journal |
| issn | 1601-5223 |
| language | English |
| last_indexed | 2024-03-12T22:16:38Z |
| publishDate | 2023-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Hereditas |
| spelling | doaj.art-32cdbdd5da694115a04d9be5fcb8e7692023-07-23T11:16:22ZengBMCHereditas1601-52232023-07-01160111510.1186/s41065-023-00288-7An 8-gene predicting survival model of hepatocellular carcinoma (HCC) related to pyroptosis and cuproptosisHongjin Wang0Nian Wang1Ze Tang2Qiuyu Liu3Shiyu Nie4Wu Tao5Department of Critical Care Medicine, Yongchuan Hospital, Chongqing Medical UniversityDepartment of Critical Care Medicine, Yongchuan Hospital, Chongqing Medical UniversityDepartment of Critical Care Medicine, Yongchuan Hospital, Chongqing Medical UniversityDepartment of Critical Care Medicine, Yongchuan Hospital, Chongqing Medical UniversityDepartment of Critical Care Medicine, Yongchuan Hospital, Chongqing Medical UniversityDepartment of Critical Care Medicine, Yongchuan Hospital, Chongqing Medical UniversityAbstract Background The study aimed to establish a prognostic survival model with 8 pyroptosis-and-cuproptosis-related genes to examine the prognostic effect in patients of hepatocellular carcinoma (HCC). Methods We downloaded gene expression data and clinical information of HCC patients from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO). The clustering analysis and cox regression with LASSO were used for constructing an 8 PCmRNAs survival model. Using TCGA, ICGC and GEO cohort, the overall survival (OS) between high- and low- risk group was determined. We also evaluated independent prognostic indicators using univariate and multivariate analyses. The relatively bioinformatics analysis, including immune cell infiltration, function enrichment and drug sensitivity analyses, was performed as well. The gene expression of 8 PCmRNAs in vitro were validated in several HCC cell lines by qRT-PCR and Western blot. The relationship between GZMA and Fludarabine were further checked by CCK-8 assay. Results The survival prognostic model was constructed with ATP7A, GLS, CDKN2A, BAK1, CHMP4B, NLRP6, NOD1 and GZMA using data from TCGA cohort. The ICGC and GEO cohort were used for model validation. Receiver operating characteristic (ROC) curves showed a good survival prediction by this model. Risk scores had the highest predictable value for survival among Stage, Age, Gender and Grade. Most Immune cells and immune functions were decreased in high-risk group. Besides, function enrichment analyses showed that steroid metabolic process, hormone metabolic process, collagen − containing extracellular matrix, oxidoreductase activity and pyruvate metabolism were enriched. Potential drugs targeted different PCDEGs like Nelarabine, Dexamethasone and Fludarabine were found as well. ATP7A, GLS, CDKN2A, BAK1, CHMP4B, NOD1 were upregulated while NLRP6 and GZMA were downregulated in most HCC cell lines. The potential therapy of Fludarabine was demonstrated when GZMA was low expressed in Huh7 cell line. Conclusion We constructed a novel 8-gene (ATP7A, GLS, CDKN2A, BAK1, CHMP4B, NLRP6, NOD1 and GZMA) prognostic model and explored potential functional information and microenvironment of HCC, which might be worthy of clinical application. In addition, several potential chemotherapy drugs were screened and Fludarabine might be effective for HCC patients whose GZMA was low expressed.https://doi.org/10.1186/s41065-023-00288-7Hepatocellular carcinomaPrognostic modelPyroptosisCuproptosisBioinformatics |
| spellingShingle | Hongjin Wang Nian Wang Ze Tang Qiuyu Liu Shiyu Nie Wu Tao An 8-gene predicting survival model of hepatocellular carcinoma (HCC) related to pyroptosis and cuproptosis Hereditas Hepatocellular carcinoma Prognostic model Pyroptosis Cuproptosis Bioinformatics |
| title | An 8-gene predicting survival model of hepatocellular carcinoma (HCC) related to pyroptosis and cuproptosis |
| title_full | An 8-gene predicting survival model of hepatocellular carcinoma (HCC) related to pyroptosis and cuproptosis |
| title_fullStr | An 8-gene predicting survival model of hepatocellular carcinoma (HCC) related to pyroptosis and cuproptosis |
| title_full_unstemmed | An 8-gene predicting survival model of hepatocellular carcinoma (HCC) related to pyroptosis and cuproptosis |
| title_short | An 8-gene predicting survival model of hepatocellular carcinoma (HCC) related to pyroptosis and cuproptosis |
| title_sort | 8 gene predicting survival model of hepatocellular carcinoma hcc related to pyroptosis and cuproptosis |
| topic | Hepatocellular carcinoma Prognostic model Pyroptosis Cuproptosis Bioinformatics |
| url | https://doi.org/10.1186/s41065-023-00288-7 |
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