1
|
Shi Z, Liu X, Li D, Fan X, He L, Zhou D, Lin H. Construction of a prognostic model based on genome-wide methylation analysis of miRNAs for hepatocellular carcinoma. Epigenomics 2024; 16:513-527. [PMID: 38477016 PMCID: PMC11160443 DOI: 10.2217/epi-2023-0365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/08/2024] [Indexed: 03/14/2024] Open
Abstract
Aim: Using the methylation level of miRNA genes to develop a prognostic model for patients with hepatocellular carcinoma (HCC). Materials & methods: least absolute shrinkage and selection operator and multivariate Cox regression analyses were performed to develop a prognostic model. One miRNA in the model was selected for verification. Results: A prognostic model was developed using eight miRNAs. The areas under the curve for predicting overall survival at 1, 3 and 5 years were 0.75, 0.81 and 0.81. miR-223 was found to be hypomethylated in 160 HCC tissues, and its methylation level was associated with Barcelona Clinic Liver Cancer stages and the prognosis of patients with HCC. Conclusion: The prognostic model based on miRNA methylation levels has the capability to partially forecast the prognosis of patients with HCC.
Collapse
Affiliation(s)
- Zhaoqi Shi
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Xiaolong Liu
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Duguang Li
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Xiaoxiao Fan
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Lifeng He
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Daizhan Zhou
- Life Science Research Center, The First Affiliated Hospital of Xinxiang Medical University, Weihui, 453100, Henan, China
| | - Hui Lin
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| |
Collapse
|
2
|
Li Z, Lei G, Meng X, Yang Z. Identification of a new five-gene risk score for risk stratification and prognosis prediction in HCC. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 41:736-754. [PMID: 35532340 DOI: 10.1080/15257770.2022.2071445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Approximately 80% of primary liver cancer (PLC) is hepatocellular carcinoma (HCC), and the prognosis of HCC patients is unfavorable. Further studies are required to develop new prognostic tools for predicting the HCC patients' prognosis. The univariate Cox and LASSO regression were utilized to develop the multi-gene risk score. Single-sample Gene Set Enrichment Analysis (ssGSEA) was employed to assess differences of immune functions and cells. The model performance was evaluated by calibration curve and receiver operating characteristic curve (ROC). And qRT-PCR was utilized to evaluate the genes expression in clinical samples. Finally, a novel five-gene (KIF20A, CENPA, HMMR, G6PD, and ADH4) risk score was developed. Based on the median value of patients' risk scores, patients were divided into two groups: high-risk group and low-risk group. The Overall survival (OS) of patients in high-risk group was obviously poorer than that in the low-risk group. And the five-gene risk score was an independent risk factor correlated with patients' OS. Besides, a nomogram consisting of TNM stage and risk score was established. The results of decision curve, calibration curve, and ROC presented that the prognostic risk score and the nomogram had great predictive capability. Besides, ADH4's mRNA was reduced in HCC tissues, while the mRNA of KIF20A, CENPA, HMMR, and G6PD were overexpressed in HCC tissues. We developed a novel five-gene risk score that could predict HCC patients' prognosis. And these five genes could be promising therapeutic targets for HCC. The five-gene risk score and nomogram may be useful prognostic tools for HCC.
Collapse
Affiliation(s)
- Zhi Li
- Medical School of Chinese PLA and Faculty of Hepato-Pancreato-Biliary Surgery, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Guanglin Lei
- Department of Hepatology, the Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xuan Meng
- Hepatobiliary Surgery Department, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Hepatobiliary Surgery Department, Hebei Cancer Hospital, Chinese Academy of Medical Sciences, Langfang, Hebei, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical College, Xuzhou, Jiangsu, China
| | - Zhanyu Yang
- Medical School of Chinese PLA and Faculty of Hepato-Pancreato-Biliary Surgery, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| |
Collapse
|
3
|
Zhu Z, Song M, Li W, Li M, Chen S, Chen B. Identification, Verification and Pathway Enrichment Analysis of Prognosis-Related Immune Genes in Patients With Hepatocellular Carcinoma. Front Oncol 2021; 11:695001. [PMID: 34616672 PMCID: PMC8488301 DOI: 10.3389/fonc.2021.695001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 09/02/2021] [Indexed: 11/21/2022] Open
Abstract
Hepatocellular carcinoma is a common malignant tumor with poor prognosis, poor treatment effect, and lack of effective biomarkers. In this study, bioinformatics analysis of immune-related genes of hepatocellular carcinoma was used to construct a multi-gene combined marker that can predict the prognosis of patients. The RNA expression data of hepatocellular carcinoma were downloaded from The Cancer Genome Atlas (TCGA) database, and immune-related genes were obtained from the IMMPORT database. Differential analysis was performed by Wilcox test to obtain differentially expressed genes. Univariate Cox regression analysis, lasso regression analysis and multivariate Cox regression analysis were performed to establish a prognostic model of immune genes, a total of 5 genes (HDAC1, BIRC5, SPP1, STC2, NR6A1) were identified to construct the models. The expression levels of 5 genes in HCC tissues were significantly different from those in paracancerous tissues. The Kaplan-Meier survival curve showed that the risk score calculated according to the prognostic model was significantly related to the overall survival (OS) of HCC. The receiver operating characteristic (ROC) curve confirmed that the prognostic model had high accuracy. Independent prognostic analysis was performed to prove that the risk value can be used as an independent prognostic factor. Then, the gene expression data of hepatocellular carcinoma in the ICGC database was used as a validation data set for the verification of the above steps. In addition, we used the CIBERSORT software and TIMER database to conduct immune infiltration research, and the results showed that the five genes of the model and the risk score have a certain correlation with the content of immune cells. Moreover, through Gene Set Enrichment Analysis (GSEA) and the construction of protein interaction networks, we found that the p53-mediated signal transduction pathway is a potentially important signal pathway for hepatocellular carcinoma and is positively regulated by certain genes in the prognostic model. In conclusion, this study provides potential targets for predicting the prognosis and treatment of hepatocellular carcinoma patients, and also provides new ideas about the correlation between immune genes and potential pathways of hepatocellular carcinoma.
Collapse
Affiliation(s)
- Zhipeng Zhu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Department of Clinical Medicine, The First Clinical College, Anhui Medical University, Hefei, China
| | - Mengyu Song
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Department of Clinical Medicine, The First Clinical College, Anhui Medical University, Hefei, China
| | - Wenhao Li
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Department of Clinical Medicine, The First Clinical College, Anhui Medical University, Hefei, China
| | - Mengying Li
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Department of Clinical Medicine, The First Clinical College, Anhui Medical University, Hefei, China
| | - Sihan Chen
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Bo Chen
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| |
Collapse
|
4
|
Liu G, Wu D, Wen Y, Cang S. Immune-associated molecular occurrence and prognosis predictor of hepatocellular carcinoma: an integrated analysis of GEO datasets. Bioengineered 2021; 12:5253-5265. [PMID: 34424809 PMCID: PMC8806587 DOI: 10.1080/21655979.2021.1962147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the fifth most common cancer and the second most common cause of cancer-related deaths worldwide. As immune response failure is the main factor in the occurrence and poor prognosis of HCC, our study aimed to develop an immune-associated molecular occurrence and prognosis predictor (IMOPP) of HCC. To that end, we discovered a 4-gene immune-associated gene signature: C-C motif chemokine ligand 14 (CCL14), kallikrein B1 (KLKB1), vasoactive intestinal peptide receptor 1 (VIPR1), and cluster of differentiation 4 (CD4). When tested on three cohorts as an immune-associated molecular occurrence predictor (IMOP), it had high sensitivity, specificity, and area under the receiver operating characteristics curve. When tested as an immune-associated molecular prognosis predictor (IMPP), it stratified the HCC prognosis for overall survival (Kaplan-Meier analysis, log rank P = 0.0016; Cox regression, HR = 1.832, 95% CI = 1.173-2.859, P = 0.008) and disease-free survival (Kaplan-Meier analysis, log rank P = 0.0227). IMPP also significantly correlated with the clinicopathological characteristics of HCC; integrating it with clinicopathological characteristics improved the accuracy of a nomogram for overall survival prediction (C-index: 0.7097 vs. 0.6631). In HCC tumor microenviroments, the proportion of CD8+ T cells significantly differed between IMOP-stratified groups. We conclude that IMOPP can potentially predict the occurrence of HCC in high-risk populations and improve prognostic accuracy by providing new biomarkers for risk stratification. In addition, we believe that the IMOP mechanism may be related to its effect on the proportion of CD8+ T cells in tumor-infiltrating lymphocytes.
Collapse
Affiliation(s)
- Guanjun Liu
- Department of Oncology, Henan Provincial People's Hospital, Zhengzhou, Henan, P.R. China.,Department of Oncology, People's Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China.,Department of Oncology, People's Hospital of Henan University, Zhengzhou, Henan, P.R. China
| | - Dongmei Wu
- Department of Radiotherapy, Xinxiang Center Hospital, Xinxiang, Henan, P.R. China
| | - Yiyang Wen
- Department of Oncology, Henan Provincial People's Hospital, Zhengzhou, Henan, P.R. China.,Department of Oncology, People's Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China.,Department of Oncology, People's Hospital of Henan University, Zhengzhou, Henan, P.R. China
| | - Shundong Cang
- Department of Oncology, Henan Provincial People's Hospital, Zhengzhou, Henan, P.R. China.,Department of Oncology, People's Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China.,Department of Oncology, People's Hospital of Henan University, Zhengzhou, Henan, P.R. China
| |
Collapse
|
5
|
Yang L, Yin W, Liu X, Li F, Ma L, Wang D, Li H. Identification of a five-gene signature in association with overall survival for hepatocellular carcinoma. PeerJ 2021; 9:e11273. [PMID: 33986994 PMCID: PMC8088210 DOI: 10.7717/peerj.11273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/23/2021] [Indexed: 12/24/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is considered to be a malignant tumor with a high incidence and a high mortality. Accurate prognostic models are urgently needed. The present study was aimed at screening the critical genes for prognosis of HCC. Methods The GSE25097, GSE14520, GSE36376 and GSE76427 datasets were obtained from Gene Expression Omnibus (GEO). We used GEO2R to screen differentially expressed genes (DEGs). A protein-protein interaction network of the DEGs was constructed by Cytoscape in order to find hub genes by module analysis. The Metascape was performed to discover biological functions and pathway enrichment of DEGs. MCODE components were calculated to construct a module complex of DEGs. Then, gene set enrichment analysis (GSEA) was used for gene enrichment analysis. ONCOMINE was employed to assess the mRNA expression levels of key genes in HCC, and the survival analysis was conducted using the array from The Cancer Genome Atlas (TCGA) of HCC. Then, the LASSO Cox regression model was performed to establish and identify the prognostic gene signature. We validated the prognostic value of the gene signature in the TCGA cohort. Results We screened out 10 hub genes which were all up-regulated in HCC tissue. They mainly enrich in mitotic cell cycle process. The GSEA results showed that these data sets had good enrichment score and significance in the cell cycle pathway. Each candidate gene may be an indicator of prognostic factors in the development of HCC. However, hub genes expression was weekly associated with overall survival in HCC patients. LASSO Cox regression analysis validated a five-gene signature (including CDC20, CCNB2, NCAPG, ASPM and NUSAP1). These results suggest that five-gene signature model may provide clues for clinical prognostic biomarker of HCC.
Collapse
Affiliation(s)
- Lei Yang
- Department of Histology and Embryology, Binzhou Medical University, Yantai, Shandong, China
| | - Weilong Yin
- Department of Histology and Embryology, Binzhou Medical University, Yantai, Shandong, China
| | - Xuechen Liu
- Department of Histology and Embryology, Binzhou Medical University, Yantai, Shandong, China
| | - Fangcun Li
- Department of Histology and Embryology, Binzhou Medical University, Yantai, Shandong, China
| | - Li Ma
- Department of Histology and Embryology, Binzhou Medical University, Yantai, Shandong, China
| | - Dong Wang
- Department of Histology and Embryology, Binzhou Medical University, Yantai, Shandong, China
| | - Hongxing Li
- Department of Histology and Embryology, Binzhou Medical University, Yantai, Shandong, China
| |
Collapse
|
6
|
Identification of a thirteen-gene signature predicting overall survival for hepatocellular carcinoma. Biosci Rep 2021; 41:228241. [PMID: 33835133 PMCID: PMC8065179 DOI: 10.1042/bsr20202870] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 02/23/2021] [Accepted: 03/19/2021] [Indexed: 01/21/2023] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is a malignant tumor of the digestive system characterized by mortality rate and poor prognosis. To indicate the prognosis of HCC patients, lots of genes have been screened as prognostic indicators. However, the predictive efficiency of single gene is not enough. Therefore, it is essential to identify a risk-score model based on gene signature to elevate predictive efficiency. Methods: Lasso regression analysis followed by univariate Cox regression was employed to establish a risk-score model for HCC prognosis prediction based on The Cancer Genome Atlas (TCGA) dataset and Gene Expression Omnibus (GEO) dataset GSE14520. R package ‘clusterProfiler’ was used to conduct function and pathway enrichment analysis. The infiltration level of various immune and stromal cells in the tumor microenvironment (TME) were evaluated by single-sample GSEA (ssGSEA) of R package ‘GSVA’. Results: This prognostic model is an independent prognostic factor for predicting the prognosis of HCC patients and can be more effective by combining with clinical data through the construction of nomogram model. Further analysis showed patients in high-risk group possess more complex TME and immune cell composition. Conclusions: Taken together, our research suggests the thirteen-gene signature to possess potential prognostic value for HCC patients and provide new information for immunological research and treatment in HCC.
Collapse
|
7
|
Kang H, Wang N, Wang X, Zhang Y, Lin S, Mao G, Liu D, Dang C, Zhou Z. A glycolysis-related gene signature predicts prognosis of patients with esophageal adenocarcinoma. Aging (Albany NY) 2020; 12:25828-25844. [PMID: 33234735 PMCID: PMC7803571 DOI: 10.18632/aging.104206] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 09/29/2020] [Indexed: 12/14/2022]
Abstract
Background: Esophageal adenocarcinoma (EAC) is a growing problem with a rapidly rising incidence and carries a poor prognosis. We aimed to develop a glycolysis-related gene signature to predict the prognostic outcome of patients with EAC. Results: Five genes (CLDN9, GFPT1, HMMR, RARS and STMN1) were correlated with prognosis of EAC patients. Patients were classified into high-risk and low-risk groups calculated by Cox regression analysis, based on the five gene signature risk score. The five-gene signature was an independent biomarker for prognosis and patients with low risk scores showed better prognosis. Nomogram incorporating the gene signature and clinical prognostic factors was effective in predicting the overall survival. Conclusion: An innovative identified glycolysis-related gene signature and an effective nomogram reliably predicted the prognosis of EAC patients. Methods: The Cancer Genome Atlas database was investigated for the gene expression profile of EAC patients. Glycolytic gene sets difference between EAC and normal tissues were identified via Gene set enrichment analysis (GSEA). Univariate and multivariate Cox analysis were utilized to construct a prognostic gene signature. The signature was evaluated by receiver operating characteristic curves and Kaplan–Meier curves. A prognosis model integrating clinical parameters with the gene signature was established with nomogram.
Collapse
Affiliation(s)
- Huafeng Kang
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi'an, China
| | - Nan Wang
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi'an, China
| | - Xuan Wang
- Department of Surgical Oncology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi'an, China
| | - Yu Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi'an, China
| | - Shuai Lin
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi'an, China
| | - Guochao Mao
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi'an, China
| | - Di Liu
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi'an, China
| | - Chengxue Dang
- Department of Surgical Oncology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi'an, China
| | - Zhangjian Zhou
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi'an, China
| |
Collapse
|
8
|
Zhou W, Zhang S, Cai Z, Gao F, Deng W, Wen Y, Qiu ZW, Hou ZK, Chen XL. A glycolysis-related gene pairs signature predicts prognosis in patients with hepatocellular carcinoma. PeerJ 2020; 8:e9944. [PMID: 33062428 PMCID: PMC7531359 DOI: 10.7717/peerj.9944] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 08/24/2020] [Indexed: 12/24/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is one of the most universal malignant liver tumors worldwide. However, there were no systematic studies to establish glycolysis‑related gene pairs (GRGPs) signatures for the patients with HCC. Therefore, the study aimed to establish novel GRGPs signatures to better predict the prognosis of HCC. Methods Based on the data from Gene Expression Omnibus, The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium databases, glycolysis-related mRNAs were used to construct GRGPs. Cox regression was applied to establish a seventeen GRGPs signature in TCGA dataset, which was verified in two validation (European and American, and Asian) datasets. Results Seventeen prognostic GRGPs (HMMR_PFKFB1, CHST1_GYS2, MERTK_GYS2, GPC1_GYS2, LDHA_GOT2, IDUA_GNPDA1, IDUA_ME2, IDUA_G6PD, IDUA_GPC1, MPI_GPC1, SDC2_LDHA, PRPS1_PLOD2, GALK1_IER3, MET_PLOD2, GUSB_IGFBP3, IL13RA1_IGFBP3 and CYB5A_IGFBP3) were identified to be significantly progressive factors for the patients with HCC in the TCGA dataset, which constituted a GRGPs signature. The patients with HCC were classified into low-risk group and high-risk group based on the GRGPs signature. The GRGPs signature was a significantly independent prognostic indicator for the patients with HCC in TCGA (log-rank P = 2.898e−14). Consistent with the TCGA dataset, the patients in low-risk group had a longer OS in two validation datasets (European and American: P = 1.143e−02, and Asian: P = 6.342e−08). Additionally, the GRGPs signature was also validated as a significantly independent prognostic indicator in two validation datasets. Conclusion The seventeen GRGPs and their signature might be molecular biomarkers and therapeutic targets for the patients with HCC.
Collapse
Affiliation(s)
- Weige Zhou
- School of Basic Medical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shijing Zhang
- School of Basic Medical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zheyou Cai
- School of Basic Medical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Fei Gao
- Department of Minimally Invasive & Interventional Radiology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wenhui Deng
- The Fourth Affiliated Hospital of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Yi Wen
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhen-Wen Qiu
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zheng-Kun Hou
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xin-Lin Chen
- School of Basic Medical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
| |
Collapse
|
9
|
Zhou T, Cai Z, Ma N, Xie W, Gao C, Huang M, Bai Y, Ni Y, Tang Y. A Novel Ten-Gene Signature Predicting Prognosis in Hepatocellular Carcinoma. Front Cell Dev Biol 2020; 8:629. [PMID: 32760725 PMCID: PMC7372135 DOI: 10.3389/fcell.2020.00629] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/23/2020] [Indexed: 01/27/2023] Open
Abstract
Hepatocellular carcinoma (HCC) has a dismal long-term outcome. We aimed to construct a multi-gene model for prognosis prediction to inform HCC management. The cancer-specific differentially expressed genes (DEGs) were identified using RNA-seq data of paired tumor and normal tissue. A prognostic signature was built by LASSO regression analysis. Gene set enrichment analysis (GSEA) was performed to further understand the underlying molecular mechanisms. A 10-gene signature was constructed to stratify the TCGA and ICGC cohorts into high- and low-risk groups where prognosis was significantly worse in the high-risk group across cohorts (P < 0.001 for all). The 10-gene signature outperformed all previously reported models for both C-index and the AUCs for 1-, 3-, 5-year survival prediction (C-index, 0.84 vs 0.67 to 0.73; AUCs for 1-, 3- and 5-year OS, 0.84 vs 0.68 to 0.79, 0.81 to 0.68 to 0.80, and 0.85 vs 0.67 to 0.78, respectively). Multivariate Cox regression analysis revealed risk group and tumor stage to be independent predictors of survival in HCC. A nomogram incorporating tumor stage and signature-based risk group showed better performance for 1- and 3-year survival than for 5-year survival. GSEA revealed enrichment of pathways related to cell cycle regulation among high-risk samples and metabolic processes in the low-risk group. Our 10-gene model is robust for prognosis prediction and may help inform clinical management of HCC.
Collapse
Affiliation(s)
- Taicheng Zhou
- Department of Gastroenterological Surgery and Hernia Center, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Supported by National Key Clinical Discipline, Guangzhou, China
| | - Zhihua Cai
- Department of Oncology, The Affiliated Cancer Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ning Ma
- Department of Gastroenterological Surgery and Hernia Center, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Supported by National Key Clinical Discipline, Guangzhou, China
| | - Wenzhuan Xie
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Chan Gao
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Mengli Huang
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Yuezong Bai
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Yangpeng Ni
- Department of Oncology, Jieyang People's Hospital, Sun Yat-sen University, Jieyang, China
| | - Yunqiang Tang
- Department of Hepatic-Biliary Surgery, The Affiliated Cancer Hospital of Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
10
|
Liu A, Wu Q, Peng D, Ares I, Anadón A, Lopez-Torres B, Martínez-Larrañaga MR, Wang X, Martínez MA. A novel strategy for the diagnosis, prognosis, treatment, and chemoresistance of hepatocellular carcinoma: DNA methylation. Med Res Rev 2020; 40:1973-2018. [PMID: 32525219 DOI: 10.1002/med.21696] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 04/29/2020] [Accepted: 05/17/2020] [Indexed: 12/11/2022]
Abstract
The cancer mortality rate of hepatocellular carcinoma (HCC) is the second highest in the world and the therapeutic options are limited. The incidence of this deadly cancer is rising at an alarming rate because of the high degree of resistance to chemo- and radiotherapy, lack of proper, and adequate vaccination to hepatitis B, and lack of consciousness and knowledge about the disease itself and the lifestyle of the people. DNA methylation and DNA methylation-induced epigenetic alterations, due to their potential reversibility, open the access to develop novel biomarkers and therapeutics for HCC. The contribution to these epigenetic changes in HCC development still has not been thoroughly summarized. Thus, it is necessary to better understand the new molecular targets of HCC epigenetics in HCC diagnosis, prevention, and treatment. This review elaborates on recent key findings regarding molecular biomarkers for HCC early diagnosis, prognosis, and treatment. Currently emerging epigenetic drugs for the treatment of HCC are summarized. In addition, combining epigenetic drugs with nonepigenetic drugs for HCC treatment is also mentioned. The molecular mechanisms of DNA methylation-mediated HCC resistance are reviewed, providing some insights into the difficulty of treating liver cancer and anticancer drug development.
Collapse
Affiliation(s)
- Aimei Liu
- National Reference Laboratory of Veterinary Drug Residues and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University (HZAU), Wuhan, China
| | - Qinghua Wu
- College of Life Science, Yangtze University, Jingzhou, China.,Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Dapeng Peng
- National Reference Laboratory of Veterinary Drug Residues and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University (HZAU), Wuhan, China
| | - Irma Ares
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Research Institute Hospital 12 de Octubre (i+12), Universidad Complutense de Madrid (UCM), Madrid, Spain
| | - Arturo Anadón
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Research Institute Hospital 12 de Octubre (i+12), Universidad Complutense de Madrid (UCM), Madrid, Spain
| | - Bernardo Lopez-Torres
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Research Institute Hospital 12 de Octubre (i+12), Universidad Complutense de Madrid (UCM), Madrid, Spain
| | - María-Rosa Martínez-Larrañaga
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Research Institute Hospital 12 de Octubre (i+12), Universidad Complutense de Madrid (UCM), Madrid, Spain
| | - Xu Wang
- National Reference Laboratory of Veterinary Drug Residues and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University (HZAU), Wuhan, China.,Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Research Institute Hospital 12 de Octubre (i+12), Universidad Complutense de Madrid (UCM), Madrid, Spain
| | - María-Aránzazu Martínez
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Research Institute Hospital 12 de Octubre (i+12), Universidad Complutense de Madrid (UCM), Madrid, Spain
| |
Collapse
|
11
|
Wang Y, Ruan Z, Yu S, Tian T, Liang X, Jing L, Li W, Wang X, Xiang L, Claret FX, Nan K, Guo H. A four-methylated mRNA signature-based risk score system predicts survival in patients with hepatocellular carcinoma. Aging (Albany NY) 2020; 11:160-173. [PMID: 30631005 PMCID: PMC6339794 DOI: 10.18632/aging.101738] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 12/19/2018] [Indexed: 01/05/2023]
Abstract
Evidence suggests that altered DNA methylation plays a causative role in the pathogenesis of various cancers, including hepatocellular carcinoma (HCC). Thus, methylated differently expressed genes (MDEGs) could potentially serve as biomarkers and therapeutic targets in HCC. In the present study, screening four genomics profiling datasets (GSE62232, GSE84402, GSE73003 and GSE57956) enabled us to identify a total of 148 MDEGs. A signature was then established based on the top four MDEGs (BRCA1, CAD, CDC20 and RBM8A). Taking clinical variables into consideration, we constructed a risk score system consisting of the four-MDEG signature and the patients' clinical features, which was predictive of prognosis in HCC. The prognostic value of the HCC risk score system was confirmed using TCGA HCC samples. The scores were then used to construct a nomogram, performance of which was evaluated using Harrel's concordance index (C-index) and a calibration curve. The signature-based nomogram for prediction of overall survival in HCC patients exhibited good performance and was superior to traditional staging systems (C-index: 0.676 vs 0.629, P< 0.05). We have thus established a novel risk score system that is predictive of prognosis and is a potentially useful guide for personalized treatment of HCC patients.
Collapse
Affiliation(s)
- Yu Wang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Zhiping Ruan
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Sizhe Yu
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Tao Tian
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Xuan Liang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Li Jing
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Wenyuan Li
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Xiao Wang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Lcl Xiang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - F X Claret
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kejun Nan
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Hui Guo
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| |
Collapse
|
12
|
Chen J, Wang X, Wang X, Li W, Shang C, Chen T, Chen Y. A FITM1-Related Methylation Signature Predicts the Prognosis of Patients With Non-Viral Hepatocellular Carcinoma. Front Genet 2020; 11:99. [PMID: 32174969 PMCID: PMC7056874 DOI: 10.3389/fgene.2020.00099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 01/29/2020] [Indexed: 12/11/2022] Open
Abstract
Although great progress has been made in treatment against hepatitis virus infection, the prognosis of hepatocellular carcinoma (HCC) remains unsatisfied. Therefore, there is an unmet need to explore biomarkers or prognostic models for monitoring non-viral hepatocellular carcinoma. Accumulating evidence indicates that DNA methylation participates in carcinogenesis of malignancies. In the present study, we analyzed 101 non-viral HCC patients from TCGA database to figure out methylation-driven genes (MDGs) that might get involved in non-viral HCC pathogenesis using MethyMix algorithm. Then we picked out 8 key genes out of 137 MDGs that could affect the overall survival (OS) of both methylation and expression level. Using PCA, Uni-variate, Multi-variate, and LASSO cox regression analyses, we confirmed the potential prognostic value of these eight epigenetic genes. Ultimately, combined with immunohistochemistry (IHC), ROC, OS, and GSEA analyses, fat storage-inducing transmembrane protein1 (FITM1) was identified as a novel tumor suppressor gene in non-viral HCC and an applicable FITM1-methylation-based signature was built in a training set and validated in a testing set. Briefly, our work provides several potential biomarkers, especially FITM1, as well as a new method for disease surveillance and treatment strategy development.
Collapse
Affiliation(s)
- Jie Chen
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xicheng Wang
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xining Wang
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wenxin Li
- Department of Cardiology, The Eight Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Changzhen Shang
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Tao Chen
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yajin Chen
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
13
|
Liu J, Lu J, Ma Z, Li W. A Nomogram Based on a Three-Gene Signature Derived from AATF Coexpressed Genes Predicts Overall Survival of Hepatocellular Carcinoma Patients. BIOMED RESEARCH INTERNATIONAL 2020; 2020:7310768. [PMID: 32382568 PMCID: PMC7195644 DOI: 10.1155/2020/7310768] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/14/2020] [Accepted: 03/16/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a common cancer with an extremely high mortality rate. Therefore, there is an urgent need in screening key biomarkers of HCC to predict the prognosis and develop more individual treatments. Recently, AATF is reported to be an important factor contributing to HCC. METHODS We aimed to establish a gene signature to predict overall survival of HCC patients. Firstly, we examined the expression level of AATF in the Gene Expression Omnibus (GEO), the Cancer Genome Atlas (TCGA), and the International Union of Cancer Genome (ICGC) databases. Genes coexpressed with AATF were identified in the TCGA dataset by the Poisson correlation coefficient and used to establish a gene signature for survival prediction. The prognostic significance of this gene signature was then validated in the ICGC dataset and used to build a combined prognostic model for clinical practice. RESULTS Gene expression data and clinical information of 2521 HCC patients were downloaded from three public databases. AATF expression in HCC tissue was higher than that in matched normal liver tissues. 644 genes coexpressed with AATF were identified by the Poisson correlation coefficient and used to establish a three-gene signature (KIF20A, UCK2, and SLC41A3) by the univariate and multivariate least absolute shrinkage and selection operator Cox regression analyses. This three-gene signature was then used to build a combined nomogram for clinical practice. CONCLUSION This integrated nomogram based on the three-gene signature can predict overall survival for HCC patients well. The three-gene signature may be a potential therapeutic target in HCC.
Collapse
Affiliation(s)
- Jun Liu
- Departments of Clinical Laboratory, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan, Guangdong, China
| | - Jianjun Lu
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, China
- Department of Medical Services, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhanzhong Ma
- Departments of Clinical Laboratory, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan, Guangdong, China
| | - Wenli Li
- Departments of Clinical Laboratory, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan, Guangdong, China
- Departments of Reproductive Medicine Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan, Guangdong, China
| |
Collapse
|
14
|
Zhang L, Zhang Z, Yu Z. Identification of a novel glycolysis-related gene signature for predicting metastasis and survival in patients with lung adenocarcinoma. J Transl Med 2019; 17:423. [PMID: 31847905 PMCID: PMC6916245 DOI: 10.1186/s12967-019-02173-2] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 12/06/2019] [Indexed: 12/18/2022] Open
Abstract
Background Lung cancer (LC) is one of the most lethal and most prevalent malignant tumors, and its incidence and mortality are increasing annually. Lung adenocarcinoma (LUAD) is the most common pathological type of lung cancer. Several biomarkers have been confirmed by data excavation to be related to metastasis, prognosis and survival. However, the moderate predictive effect of a single gene biomarker is not sufficient. Thus, we aimed to identify new gene signatures to better predict the possibility of LUAD. Methods Using an mRNA-mining approach, we performed mRNA expression profiling in large LUAD cohorts (n = 522) from The Cancer Genome Atlas (TCGA) database. Gene Set Enrichment Analysis (GSEA) was performed, and connections between genes and glycolysis were found in the Cox proportional regression model. Results We confirmed a set of nine genes (HMMR, B4GALT1, SLC16A3, ANGPTL4, EXT1, GPC1, RBCK1, SOD1, and AGRN) that were significantly associated with metastasis and overall survival (OS) in the test series. Based on this nine-gene signature, the patients in the test series could be divided into high-risk and low-risk groups. Additionally, multivariate Cox regression analysis revealed that the prognostic power of the nine-gene signature is independent of clinical factors. Conclusion Our study reveals a connection between the nine-gene signature and glycolysis. This research also provides novel insights into the mechanisms underlying glycolysis and offers a novel biomarker of a poor prognosis and metastasis for LUAD patients.
Collapse
Affiliation(s)
- Lei Zhang
- Department of Breast Surgery, The First Hospital Affiliated China Medical University, No. 155 Nanjing Street, Heping District, Shenyang, 110001, Liaoning, China
| | - Zhe Zhang
- Department of Thoracic Surgery, The First Hospital Affiliated China Medical University, No. 155 Nanjing Street, Heping District, Shenyang, 110001, Liaoning, China
| | - Zhenglun Yu
- Department of Thoracic Surgery, The First Hospital Affiliated China Medical University, No. 155 Nanjing Street, Heping District, Shenyang, 110001, Liaoning, China.
| |
Collapse
|
15
|
Wang ZH, Zhang YZ, Wang YS, Ma XX. Identification of novel cell glycolysis related gene signature predicting survival in patients with endometrial cancer. Cancer Cell Int 2019; 19:296. [PMID: 31807118 PMCID: PMC6857303 DOI: 10.1186/s12935-019-1001-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 10/24/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Endometrial cancer (EC) is one of the three major gynecological malignancies. Numerous biomarkers that may be associated with survival and prognosis have been identified through database mining in previous studies. However, the predictive ability of single-gene biomarkers is not sufficiently specific. Genetic signatures may be an improved option for prediction. This study aimed to explore data from The Cancer Genome Atlas (TCGA) to identify a new genetic signature for predicting the prognosis of EC. METHODS mRNA expression profiling was performed in a group of patients with EC (n = 548) from TCGA. Gene set enrichment analysis was performed to identify gene sets that were significantly different between EC tissues and normal tissues. Cox proportional hazards regression models were used to identify genes significantly associated with overall survival. Quantitative real-time-PCR was used to verify the reliability of the expression of selected mRNAs. Subsequent multivariate Cox regression analysis was used to establish a prognostic risk parameter formula. Kaplan-Meier survival estimates and the log-rank test were used to validate the significance of risk parameters for prognosis prediction. RESULT Nine genes associated with glycolysis (CLDN9, B4GALT1, GMPPB, B4GALT4, AK4, CHST6, PC, GPC1, and SRD5A3) were found to be significantly related to overall survival. The results of mRNA expression analysis by PCR were consistent with those of bioinformatics analysis. Based on the nine-gene signature, the 548 patients with EC were divided into high/low-risk subgroups. The prognostic ability of the nine-gene signature was not affected by other factors. CONCLUSION A nine-gene signature associated with cellular glycolysis for predicting the survival of patients with EC was developed. The findings provide insight into the mechanisms of cellular glycolysis and identification of patients with poor prognosis in EC.
Collapse
Affiliation(s)
- Zi-Hao Wang
- Department of Obstetrics and Gynecology, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shengjing Hospital of China Medical University, 39 Huaxiang Road, Shenyang, 110021 People’s Republic of China
| | - Yun-Zheng Zhang
- Department of Obstetrics and Gynecology, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shengjing Hospital of China Medical University, 39 Huaxiang Road, Shenyang, 110021 People’s Republic of China
| | - Yu-Shan Wang
- Department of Obstetrics and Gynecology, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shengjing Hospital of China Medical University, 39 Huaxiang Road, Shenyang, 110021 People’s Republic of China
| | - Xiao-Xin Ma
- Department of Obstetrics and Gynecology, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shengjing Hospital of China Medical University, 39 Huaxiang Road, Shenyang, 110021 People’s Republic of China
| |
Collapse
|
16
|
Liu GM, Zeng HD, Zhang CY, Xu JW. Identification of a six-gene signature predicting overall survival for hepatocellular carcinoma. Cancer Cell Int 2019; 19:138. [PMID: 31139015 PMCID: PMC6528264 DOI: 10.1186/s12935-019-0858-2] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 05/13/2019] [Indexed: 02/08/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) remains a major challenge for public health worldwide. Considering the great heterogeneity of HCC, more accurate prognostic models are urgently needed. To identify a robust prognostic gene signature, we conduct this study. Materials and methods Level 3 mRNA expression profiles and clinicopathological data were obtained in The Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA-LIHC). GSE14520 dataset from the gene expression omnibus (GEO) database was downloaded to further validate the results in TCGA. Differentially expressed mRNAs between HCC and normal tissue were investigated. Univariate Cox regression analysis and lasso Cox regression model were performed to identify and construct the prognostic gene signature. Time-dependent receiver operating characteristic (ROC), Kaplan–Meier curve, multivariate Cox regression analysis, nomogram, and decision curve analysis (DCA) were used to assess the prognostic capacity of the six-gene signature. The prognostic value of the gene signature was further validated in independent GSE14520 cohort. Gene Set Enrichment Analyses (GSEA) was performed to further understand the underlying molecular mechanisms. The performance of the prognostic signature in differentiating between normal liver tissues and HCC were also investigated. Results A novel six-gene signature (including CSE1L, CSTB, MTHFR, DAGLA, MMP10, and GYS2) was established for HCC prognosis prediction. The ROC curve showed good performance in survival prediction in both the TCGA HCC cohort and the GSE14520 validation cohort. The six-gene signature could stratify patients into a high- and low-risk group which had significantly different survival. Cox regression analysis showed that the six-gene signature could independently predict OS. Nomogram including the six-gene signature was established and shown some clinical net benefit. Furthermore, GSEA revealed several significantly enriched oncological signatures and various metabolic process, which might help explain the underlying molecular mechanisms. Besides, the prognostic signature showed a strong ability for differentiating HCC from normal tissues. Conclusions Our study established a novel six-gene signature and nomogram to predict overall survival of HCC, which may help in clinical decision making for individual treatment. Electronic supplementary material The online version of this article (10.1186/s12935-019-0858-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Gao-Min Liu
- Department of Hepatobiliary Surgery, Meizhou People's Hospital, No. 38 Huangtang Road, Meizhou, 514000 China
| | - Hua-Dong Zeng
- Department of Hepatobiliary Surgery, Meizhou People's Hospital, No. 38 Huangtang Road, Meizhou, 514000 China
| | - Cai-Yun Zhang
- Department of Hepatobiliary Surgery, Meizhou People's Hospital, No. 38 Huangtang Road, Meizhou, 514000 China
| | - Ji-Wei Xu
- Department of Hepatobiliary Surgery, Meizhou People's Hospital, No. 38 Huangtang Road, Meizhou, 514000 China
| |
Collapse
|
17
|
Zhao L, Jiang L, He L, Wei Q, Bi J, Wang Y, Yu L, He M, Zhao L, Wei M. Identification of a novel cell cycle-related gene signature predicting survival in patients with gastric cancer. J Cell Physiol 2018; 234:6350-6360. [PMID: 30238991 DOI: 10.1002/jcp.27365] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 08/17/2018] [Indexed: 12/15/2022]
Abstract
Gastric cancer (GC) is one of the most fatal cancers in the world. Thousands of biomarkers have been explored that might be related to survival and prognosis via database mining. However, the prediction effect of single gene biomarkers is not specific enough. Increasing evidence suggests that gene signatures are emerging as a possible better alternative. We aimed to develop a novel gene signature to improve the prognosis prediction of GC. Using the messenger RNA (mRNA)-mining approach, we performed mRNA expression profiling in a large GC cohort (n = 375) from The Cancer Genome Atlas (TCGA) database. Gene Set Enrichment Analysis (GSEA) was performed, and we recovered genes related to the G2/M checkpoint, which we identified with a Cox proportional regression model. We identified a set of five genes (MARCKS, CCNF, MAPK14, INCENP, and CHAF1A), which were significantly associated with overall survival (OS) in the test series. Based on this five-gene signature, the test series patients could be classified into high-risk or low-risk subgroups. Multivariate Cox regression analysis indicated that the prognostic power of this five-gene signature was independent of clinical features. In conclusion, we developed a five-gene signature related to the cell cycle that can predict survival for GC. Our findings provide novel insight that is useful for understanding cell cycle mechanisms and for identifying patients with GC with poor prognoses.
Collapse
Affiliation(s)
- Lan Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Longyang Jiang
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Linxiu He
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Qian Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Jia Bi
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Yan Wang
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Lifeng Yu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Miao He
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Lin Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| |
Collapse
|