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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.
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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
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2
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Tao S, Liang S, Zeng T, Yin D. Epigenetic modification-related mechanisms of hepatocellular carcinoma resistance to immune checkpoint inhibition. Front Immunol 2023; 13:1043667. [PMID: 36685594 PMCID: PMC9845774 DOI: 10.3389/fimmu.2022.1043667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/28/2022] [Indexed: 01/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) constitutes most primary liver cancers and is one of the most lethal and life-threatening malignancies globally. Unfortunately, a substantial proportion of HCC patients are identified at an advanced stage that is unavailable for curative surgery. Thus, palliative therapies represented by multi-tyrosine kinase inhibitors (TKIs) sorafenib remained the front-line treatment over the past decades. Recently, the application of immune checkpoint inhibitors (ICIs), especially targeting the PD-1/PD-L1/CTLA-4 axis, has achieved an inspiring clinical breakthrough for treating unresectable solid tumors. However, many HCC patients with poor responses lead to limited benefits in clinical applications, which has quickly drawn researchers' attention to the regulatory mechanisms of immune checkpoints in HCC immune evasion. Evasion of immune surveillance by cancer is attributed to intricate reprogramming modulation in the tumor microenvironment. Currently, more and more studies have found that epigenetic modifications, such as chromatin structure remodeling, DNA methylation, histone post-translational modifications, and non-coding RNA levels, may contribute significantly to remodeling the tumor microenvironment to avoid immune clearance, affecting the efficacy of immunotherapy for HCC. This review summarizes the rapidly emerging progress of epigenetic-related changes during HCC resistance to ICIs and discusses the mechanisms of underlying epigenetic therapies available for surmounting immune resistance. Finally, we summarize the clinical advances in combining epigenetic therapies with immunotherapy, aiming to promote the formation of immune combination therapy strategies.
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Affiliation(s)
- Shengwei Tao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Shuhang Liang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Taofei Zeng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Dalong Yin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
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Liu J, Lu J, Li W, Mao W, Lu Y. Machine Learning Screens Potential Drugs Targeting a Prognostic Gene Signature Associated With Proliferation in Hepatocellular Carcinoma. Front Genet 2022; 13:900380. [PMID: 35836576 PMCID: PMC9273781 DOI: 10.3389/fgene.2022.900380] [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: 04/08/2022] [Accepted: 06/13/2022] [Indexed: 02/05/2023] Open
Abstract
Background: This study aimed to screen potential drugs targeting a new prognostic gene signature associated with proliferation in hepatocellular carcinoma (HCC). Methods: CRISPR Library and TCGA datasets were used to explore differentially expressed genes (DEGs) related to the proliferation of HCC cells. Differential gene expression analysis, univariate COX regression analysis, random forest algorithm and multiple combinatorial screening were used to construct a prognostic gene signature. Then the predictive power of the gene signature was validated in the TCGA and ICGC datasets. Furthermore, potential drugs targeting this gene signature were screened. Results: A total of 640 DEGs related to HCC proliferation were identified. Using univariate Cox analysis and random forest algorithm, 10 hub genes were screened. Subsequently, using multiplex combinatorial screening, five hub genes (FARSB, NOP58, CCT4, DHX37 and YARS) were identified. Taking the median risk score as a cutoff value, HCC patients were divided into high- and low-risk groups. Kaplan-Meier analysis performed in the training set showed that the overall survival of the high-risk group was worse than that of the low-risk group (p < 0.001). The ROC curve showed a good predictive efficiency of the risk score (AUC > 0.699). The risk score was related to gene mutation, cancer cell stemness and immune function changes. Prediction of immunotherapy suggetsted the IC50s of immune checkpoint inhibitors including A-443654, ABT-888, AG-014699, ATRA, AUY-922, and AZ-628 in the high-risk group were lower than those in the low-risk group, while the IC50s of AMG-706, A-770041, AICAR, AKT inhibitor VIII, Axitinib, and AZD-0530 in the high-risk group were higher than those in the low-risk group. Drug sensitivity analysis indicated that FARSB was positively correlated with Hydroxyurea, Vorinostat, Nelarabine, and Lomustine, while negatively correlated with JNJ-42756493. DHX37 was positively correlated with Raltitrexed, Cytarabine, Cisplatin, Tiotepa, and Triethylene Melamine. YARS was positively correlated with Axitinib, Fluphenazine and Megestrol acetate. NOP58 was positively correlated with Vorinostat and 6-thioguanine. CCT4 was positively correlated with Nerabine. Conclusion: The five-gene signature associated with proliferation can be used for survival prediction and risk stratification for HCC patients. Potential drugs targeting this gene signature deserve further attention in the treatment of HCC.
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Affiliation(s)
- Jun Liu
- Department of Clinical Laboratory, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
- Medical Research Center, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
| | - Jianjun Lu
- Department of Medical Affairs, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wenli Li
- Reproductive Medicine Center, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
| | - Wenjie Mao
- Emergency Department, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
| | - Yamin Lu
- Department of Clinical Laboratory, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
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4
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Fu J, Qin W, Tong Q, Li Z, Shao Y, Liu Z, Liu C, Wang Z, Xu X. A novel DNA methylation-driver gene signature for long-term survival prediction of hepatitis-positive hepatocellular carcinoma patients. Cancer Med 2022; 11:4721-4735. [PMID: 35637633 PMCID: PMC9741990 DOI: 10.1002/cam4.4838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Abnormal DNA methylation is one of the most general epigenetic modifications in hepatocellular carcinoma (HCC). Recent research showed that DNA methylation was a prognostic indicator of all-cause HCC and nonviral HCC. However, whether DNA methylation-driver genes could be used for predicting survival, the probability of hepatitis-positive HCC remains unclear. METHODS In this study, DNA methylation-driver genes (MDGs) were screened by a joint analysis of methylome and transcriptome data of 142 hepatitis-positive HCC patients. Subsequently, a prognostic risk score and nomogram were constructed. Finally, correlation analyses between the risk score and signaling pathways and immunity were conducted by GSVA and CIBERSORT. RESULTS Through random forest screening and Cox progression analysis, 10 prognostic methylation-driver genes (AC008271.1, C11orf53, CASP8, F2RL2, GBP5, LUCAT1, RP11-114B7.6, RP11-149I23.3, RP11-383 J24.1, and SLC35G2) were screened out. As a result, a prognostic risk score signature was constructed. The independent value of the risk score for prognosis prediction were addressed in the TCGA-HCC and the China-HCC cohorts. Next, clinicopathological features were analyzed and HBV status and histological grade were screened to construct a nomogram together with the risk score. The prognostic efficiency of the nomogram was validated by the calibration curves and the concordance index (C index: 0.829, 95% confidence interval: 0.794-0.864), while its clinical application ability was confirmed by decision curve analysis (DCA). At last, the relationship between the risk score and signaling pathways, as well as the correlations between immune cells were elucidated preliminary. CONCLUSIONS Taken together, our study explored a novel DNA methylation-driver gene risk score signature and an efficient nomogram for long-term survival prediction of hepatitis-positive HCC patients.
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Affiliation(s)
- Jie Fu
- Department of General SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Wei Qin
- Department of General SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Qing Tong
- Department of General SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Zhenghao Li
- Department of General SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Yaoli Shao
- Department of General SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Zhiqiang Liu
- Department of General SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Chun Liu
- Department of General SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Zicheng Wang
- Department of General SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Xundi Xu
- Department of General SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of General SurgerySouth China Hospital of Shenzhen UniversityShenzhenChina
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5
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Cui M, Qu F, Wang L, Liu X, Yu J, Tang Z, Cheng D. m5C RNA methyltransferase-related gene NSUN4 stimulates malignant progression of hepatocellular carcinoma and can be a prognostic marker. Cancer Biomark 2021; 33:389-400. [PMID: 34744073 DOI: 10.3233/cbm-210154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hepatocellular carcinoma (HCC) is a cancer with relatively high mortality, yet little attention has been devoted for related prognostic biomarkers. This study analyzed differential expression of m5C RNA methyltransferase-related genes in normal samples and tumors samples in TCGA-LIHC using Wilcoxon test. K-means consensus clustering analysis was implemented to subdivide samples. Independent prognostic factors were screened by univariate and multivariate Cox regression analyses. KEGG pathway enrichment analysis was performed on the screened independent prognostic factor using GSEA tools. qPCR was conducted to test mRNA expression of key m5C RNA methyltransferase-related genes in tissues and cells. There were 7 m5C RNA methyltransferase-related genes (NOP2, NSUN4, etc.) differentially expressed in HCC tumor tissues. HCC samples were classified into 3 subgroups through clustering analysis according to the expression mode of m5C RNA methyltransferase-related genes. It was also discovered that patients in different subgroups presented significant differences in survival rate and distribution of grade. Additionally, NOP2, NSUN4 and NSUN5 expression notable varied in different grades. Through regression analyses combined with various clinical pathological factors, it was displayed that NSUN4 could work as an independent prognostic factor. KEGG analysis showed that NSUN4 mainly enriched in signaling pathways involved in ADHERENS JUNCTION, RNA DEGRADATION, MTOR SIGNALING PATHWAY, COMPLEMENT and COAGULATION CASCADES. As examined by qPCR, NSUN4 was conspicuously upregulated in HCC patient's tissues and cells. Altogether, our study preliminarily developed a novel biomarker that could be independently used in prognosis of HCC, which may provide a new direction for the study of related molecular mechanism or treatment regimen.
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Huang H, Fu J, Zhang L, Xu J, Li D, Onwuka JU, Zhang D, Zhao L, Sun S, Zhu L, Zheng T, Jia C, Cui B, Zhao Y. Integrative Analysis of Identifying Methylation-Driven Genes Signature Predicts Prognosis in Colorectal Carcinoma. Front Oncol 2021; 11:629860. [PMID: 34178621 PMCID: PMC8231008 DOI: 10.3389/fonc.2021.629860] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 05/24/2021] [Indexed: 01/20/2023] Open
Abstract
Background Aberrant DNA methylation is a critical regulator of gene expression and plays a crucial role in the occurrence, progression, and prognosis of colorectal cancer (CRC). We aimed to identify methylation-driven genes by integrative epigenetic and transcriptomic analysis to predict the prognosis of CRC patients. Methods Methylation-driven genes were selected for CRC using a MethylMix algorithm and LASSO regression screening strategy, and were further used to construct a prognostic risk-assessment model. The Cancer Genome Atlas (TCGA) database was obtained as the training set for both the screening of methylation-driven genes and the effect of genes signature on CRC prognosis. Then, the prognostic genes signature was validated in three independent expression arrays of CRC data from Gene Expression Omnibus (GEO). Results We identified 143 methylation-driven genes, of which the combination of BATF, PHYHIPL, RBP1, and PNPLA4 expression levels was screened as a better prognostic model with the best area under the curve (AUC) (AUC = 0.876). Compared with patients in the low-risk group, CRC patients in the high-risk group had significantly poorer overall survival in the training set (HR = 2.184, 95% CI: 1.404–3.396, P < 0.001). Similar results were observed in the validation set. Moreover, VanderWeele’s mediation analysis indicated that the effect of methylation on prognosis was mediated by the levels of their expression (HRindirect = 1.473, P = 0.001, Proportion mediated, 69.10%). Conclusions We identified a four-gene prognostic signature by integrative analysis and developed a risk-assessment model that is significantly associated with patients’ survival. Methylation-driven genes might be a potential prognostic signature for CRC patients.
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Affiliation(s)
- Hao Huang
- Department of Epidemiology, Public Health School of Harbin Medical University, Harbin, China
| | - Jinming Fu
- Department of Epidemiology, Public Health School of Harbin Medical University, Harbin, China
| | - Lei Zhang
- Department of Epidemiology, Public Health School of Harbin Medical University, Harbin, China
| | - Jing Xu
- Department of Epidemiology, Public Health School of Harbin Medical University, Harbin, China
| | - Dapeng Li
- Department of Epidemiology, Public Health School of Harbin Medical University, Harbin, China
| | - Justina Ucheojor Onwuka
- Department of Epidemiology, Public Health School of Harbin Medical University, Harbin, China
| | - Ding Zhang
- Department of Epidemiology, Public Health School of Harbin Medical University, Harbin, China
| | - Liyuan Zhao
- Department of Epidemiology, Public Health School of Harbin Medical University, Harbin, China
| | - Simin Sun
- Department of Epidemiology, Public Health School of Harbin Medical University, Harbin, China
| | - Lin Zhu
- Department of Epidemiology, Public Health School of Harbin Medical University, Harbin, China
| | - Ting Zheng
- Department of Epidemiology, Public Health School of Harbin Medical University, Harbin, China
| | - Chenyang Jia
- Department of Epidemiology, Public Health School of Harbin Medical University, Harbin, China
| | - Binbin Cui
- Department of Colorectal Surgery, The Third Hospital of Harbin Medical University, Harbin, China
| | - Yashuang Zhao
- Department of Epidemiology, Public Health School of Harbin Medical University, Harbin, China
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7
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Cai G, Jin G, Liang J, Li G, Chen X, Liang H, Ding Z. Pan-cancer analysis of the prognostic value of C12orf75 based on data mining. Aging (Albany NY) 2021; 13:15214-15239. [PMID: 34074799 PMCID: PMC8221310 DOI: 10.18632/aging.203081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 05/11/2021] [Indexed: 01/14/2023]
Abstract
The differential expression of chromosome 12 open reading frame 75 (C12orf75) is closely related with cancer progression. Here, we studied the expression levels of C12orf75 and investigated its prognostic value in various cancers across distinct datasets including ONCOMINE, PrognoScan, GEPIA, and TCGA. The correlation between genetic alteration of C12orf75 and immune infiltration was investigated using the cBioPortal and TIMER databases. RNA interference was used to verify the influence of C12orf75 knockdown on the biological phenotype of hepatocellular carcinoma cells. C12orf75 showed increased expression in most tested human cancers. The increased expression of C12orf75 was related with a poor prognosis in urothelial bladder carcinoma and hepatocellular liver carcinoma, but it was surprisingly converse in renal papillary cell carcinoma. In urothelial bladder carcinoma and hepatocellular liver carcinoma, we observed positive correlations between the expression of C12orf75 and the infiltration of immune cells, including B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells. The knockdown of C12orf75 in hepatocellular carcinoma cells suppressed the proliferation, migration, and invasion and arrested the cell cycle. This is the first report C12orf75 has potential as a prognostic biomarker and therapeutic target for molecularly targeted drugs in urothelial bladder carcinoma, hepatocellular liver carcinoma, and renal papillary cell carcinoma.
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Affiliation(s)
- Guangzhen Cai
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China.,Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Wuhan, Hubei, PR China.,Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei, PR China
| | - Guannan Jin
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
| | - Junnan Liang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China.,Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Wuhan, Hubei, PR China.,Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei, PR China
| | - Ganxun Li
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China.,Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Wuhan, Hubei, PR China.,Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei, PR China
| | - Xiaoping Chen
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China.,Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Wuhan, Hubei, PR China.,Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei, PR China
| | - Huifang Liang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China.,Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Wuhan, Hubei, PR China.,Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei, PR China
| | - Zeyang Ding
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China.,Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Wuhan, Hubei, PR China.,Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei, PR China
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8
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He D, Liao S, Cai L, Huang W, Xie X, You M. Integrated analysis of methylation-driven genes and pretreatment prognostic factors in patients with hepatocellular carcinoma. BMC Cancer 2021; 21:599. [PMID: 34034705 PMCID: PMC8146257 DOI: 10.1186/s12885-021-08314-5] [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: 10/19/2020] [Accepted: 05/06/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The potential reversibility of aberrant DNA methylation indicates an opportunity for oncotherapy. This study aimed to integrate methylation-driven genes and pretreatment prognostic factors and then construct a new individual prognostic model in hepatocellular carcinoma (HCC) patients. METHODS The gene methylation, gene expression dataset and clinical information of HCC patients were downloaded from The Cancer Genome Atlas (TCGA) database. Methylation-driven genes were screened with a Pearson's correlation coefficient less than - 0.3 and a P value less than 0.05. Univariable and multivariable Cox regression analyses were performed to construct a risk score model and identify independent prognostic factors from the clinical parameters of HCC patients. The least absolute shrinkage and selection operator (LASSO) technique was used to construct a nomogram that might act to predict an individual's OS, and then C-index, ROC curve and calibration plot were used to test the practicability. The correlation between clinical parameters and core methylation-driven genes of HCC patients was explored with Student's t-test. RESULTS In this study, 44 methylation-driven genes were discovered, and three prognostic signatures (LCAT, RPS6KA6, and C5orf58) were screened to construct a prognostic risk model of HCC patients. Five clinical factors, including T stage, risk score, cancer status, surgical method and new tumor events, were identified from 13 clinical parameters as pretreatment-independent prognostic factors. To avoid overfitting, LASSO analysis was used to construct a nomogram that could be used to calculate the OS in HCC patients. The C-index was superior to that from previous studies (0.75 vs 0.717, 0.676). Furthermore, LCAT was found to be correlated with T stage and new tumor events, and RPS6KA6 was found to be correlated with T stage. CONCLUSION We identified novel therapeutic targets and constructed an individual prognostic model that can be used to guide personalized treatment in HCC patients.
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Affiliation(s)
- Dongsheng He
- Department of Medical Oncology, The First Hospital of Putian, Teaching Hospital, Fujian Medical University, Putian, 351100, China
| | - Shengyin Liao
- Department of Medical Oncology, The First Hospital of Putian, Teaching Hospital, Fujian Medical University, Putian, 351100, China
| | - Lifang Cai
- Department of Medical Oncology, The First Hospital of Putian, Teaching Hospital, Fujian Medical University, Putian, 351100, China
| | - Weiming Huang
- Department of Medical Oncology, The First Hospital of Putian, Teaching Hospital, Fujian Medical University, Putian, 351100, China
| | - Xuehua Xie
- Department of Medical Oncology, The First Hospital of Putian, Teaching Hospital, Fujian Medical University, Putian, 351100, China
| | - Mengxing You
- Department of Medical Oncology, The First Hospital of Putian, Teaching Hospital, Fujian Medical University, Putian, 351100, China.
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9
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Yi PS, Hu CJ, Li CH, Yu F. Clinical value of artificial intelligence in hepatocellular carcinoma: Current status and prospect. Artif Intell Gastroenterol 2021; 2:42-55. [DOI: 10.35712/aig.v2.i2.42] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/25/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the most commonly diagnosed type of liver cancer and the fourth leading cause of cancer-related mortality worldwide. The early identification of HCC and effective treatments for it have been challenging. Due to the sufficient compensatory ability of early patients and its nonspecific symptoms, HCC is more likely to escape diagnosis in the incipient stage, during which patients can achieve a more satisfying overall survival if they undergo resection or liver transplantation. Patients at advanced stages can profit from radical therapies in a limited way. In order to improve the unfavorable prognosis of HCC, diagnostic ability and treatment efficiency must be improved. The past decade has seen rapid advancements in artificial intelligence, underlying its unique usefulness in almost every field, including that of medicine. Herein, we sought and reviewed studies that put emphasis on artificial intelligence and HCC.
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Affiliation(s)
- Peng-Sheng Yi
- Department of Hepato-Biliary-Pancreas II, Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
| | - Chen-Jun Hu
- Department of Hepato-Biliary-Pancreas II, Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
| | - Chen-Hui Li
- Department of Obstetrics and Gynecology, Nanchong Traditional Chinese Medicine Hospital, Nanchong 637000, Sichuan Province, China
| | - Fei Yu
- Department of Radiology, Yingshan County People’s Hospital, Nanchong 610041, Sichuan Province, China
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10
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Xu Z, Xu L, Liu L, Li H, Jin J, Peng M, Huang Y, Xiao H, Li Y, Guan H. A Glycolysis-Related Five-Gene Signature Predicts Biochemical Recurrence-Free Survival in Patients With Prostate Adenocarcinoma. Front Oncol 2021; 11:625452. [PMID: 33954109 PMCID: PMC8092437 DOI: 10.3389/fonc.2021.625452] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 03/22/2021] [Indexed: 12/18/2022] Open
Abstract
Prostate cancer (PCa) is one of the most frequently diagnosed cancers in males worldwide. Approximately 25% of all patients experience biochemical recurrence (BCR) after radical prostatectomy (RP) and BCR indicates increased risk for metastasis and castration resistance. PCa patients with highly glycolytic tumors have a worse prognosis. Thus, this study aimed to explore glycolysis-based predictive biomarkers for BCR. Expression data and clinical information of PCa samples were retrieved from three publicly available datasets. One from The Cancer Genome Atlas (TCGA) dataset was used as the training cohort, and two from the Gene Expression Omnibus (GEO) dataset (GSE54460 and GSE70769) were used as validation cohorts. Using the training cohort, univariate Cox regression survival analysis, robust likelihood-based survival model, and stepwise multiply Cox analysis were sequentially applied to explore predictive glycolysis-related candidates. A five-gene risk score was then constructed based on the Cox coefficient as the following: (−0.8367*GYS2) + (0.3448*STMN1) + (0.3595*PPFIA4) + (−0.1940*KDELR3) + (0.4779*ABCB6). Receiver operating characteristic curve (ROC) analysis was used to identify the optimal cut-off point, and patients were divided into low risk and high risk groups. Kaplan–Meier analysis revealed that high risk group had significantly shorter BCR free survival time as compared with that in low risk group in training and validation cohorts. In conclusion, our data support the glycolysis-based five-gene signature as a novel and robust signature for predicting BCR of PCa patients.
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Affiliation(s)
- Zijun Xu
- Department of Endocrinology and Diabetes Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Lijuan Xu
- Department of Endocrinology and Diabetes Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Liping Liu
- National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,The Translational Medicine Laboratory, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Hai Li
- Department of Endocrinology and Diabetes Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jiewen Jin
- Department of Endocrinology and Diabetes Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Miaoguan Peng
- Department of Endocrinology and Diabetes Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yanrui Huang
- Department of Endocrinology and Diabetes Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Haipeng Xiao
- Department of Endocrinology and Diabetes Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yanbing Li
- Department of Endocrinology and Diabetes Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hongyu Guan
- Department of Endocrinology and Diabetes Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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11
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A novel DNA methylation-based model that effectively predicts prognosis in hepatocellular carcinoma. Biosci Rep 2021; 41:227938. [PMID: 33634306 PMCID: PMC7955104 DOI: 10.1042/bsr20203945] [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: 11/17/2020] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 12/15/2022] Open
Abstract
PURPOSE To build a novel predictive model for hepatocellular carcinoma (HCC) patients based on DNA methylation data. METHODS Four independent DNA methylation datasets for HCC were used to screen for common differentially methylated genes (CDMGs). Gene Ontology (GO) enrichment, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were used to explore the biological roles of CDMGs in HCC. Univariate Cox analysis and least absolute shrinkage and selection operator (LASSO) Cox analysis were performed to identify survival-related CDMGs (SR-CDMGs) and to build a predictive model. The importance of this model was assessed using Cox regression analysis, propensity score-matched (PSM) analysis and stratification analysis. A validation group from the Cancer Genome Atlas (TCGA) was constructed to further validate the model. RESULTS Four SR-CDMGs were identified and used to build the predictive model. The risk score of this model was calculated as follows: risk score = (0.01489826 × methylation level of WDR69) + (0.15868618 × methylation level of HOXB4) + (0.16674959 × methylation level of CDKL2) + (0.16689301 × methylation level of HOXA10). Kaplan-Meier analysis demonstrated that patients in the low-risk group had a significantly longer overall survival (OS; log-rank P-value =0.00071). The Cox model multivariate analysis and PSM analysis identified the risk score as an independent prognostic factor (P<0.05). Stratified analysis results further confirmed this model performed well. By analyzing the validation group, the results of receiver operating characteristic (ROC) curve analysis and survival analysis further validated this model. CONCLUSION Our DNA methylation-based prognosis predictive model is effective and reliable in predicting prognosis for patients with HCC.
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12
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Ma X, Chen H, Wang G, Li L, Tao K. DNA methylation profiling to predict overall survival risk in gastric cancer: development and validation of a nomogram to optimize clinical management. J Cancer 2020; 11:4352-4365. [PMID: 32489454 PMCID: PMC7255367 DOI: 10.7150/jca.44436] [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: 01/31/2020] [Accepted: 03/27/2020] [Indexed: 01/07/2023] Open
Abstract
DNA methylation has been reported to serve an important role in the carcinogenesis and development of gastric cancer. Our aim was to systematically develop an individualized prediction model of the survival risk combing clinical and methylation factors in gastric cancer. A univariate Cox proportional risk regression analysis was used to identify the prognosis-associated methylation sites based on the differentially expressed methylation sites between early and advanced gastric cancer group, then we applied least absolute shrinkage and selection operator (LASSO) Cox regression model to screen candidate methylation sites. Subsequently, multivariate Cox proportional risk regression analysis was conducted to identify predictive signature according to the candidate sites. Relative operating characteristic curve (ROC) analysis manifested that an 11-methylation signature exhibited great predictive efficiency for 1-, 3-, 5-year survival events. Patients in the low-risk group classified according to 11-methylation signature-based risk score yield significantly better survival than that in high-risk group. Moreover, Cox regression analysis combing methylation-based risk score and other clinical factors indicated that 11-methylation signature served as an independent risk factor. The predictive value of risk score was validated in the testing dataset. In addition, a nomogram was constructed and the ROC as well as calibration plots analysis demonstrated the good performance and clinical application of the nomogram. In conclusion, the result suggested the 11-DNA methylation signature may be potentially independent prognostic marker and functioned as a significant tool for guiding the clinical prediction of gastric cancer patients' overall survival.
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Affiliation(s)
- Xianxiong Ma
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Hengyu Chen
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- NHC Key Laboratory of Hormones and Development, Tianjin Institute of Endocrinology, Tianjin Medical University Chu Hsien-I Memorial Hospital, Tianjin 300070, China
| | - Guobin Wang
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Lei Li
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Kaixiong Tao
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
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13
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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.
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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
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14
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Li H, Song M, Yang W, Cao P, Zheng L, Zuo Y. A Comparative Analysis of Single-Cell Transcriptome Identifies Reprogramming Driver Factors for Efficiency Improvement. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 19:1053-1064. [PMID: 32045876 PMCID: PMC7015826 DOI: 10.1016/j.omtn.2019.12.035] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/23/2019] [Accepted: 12/26/2019] [Indexed: 12/11/2022]
Abstract
Terminally differentiated somatic cells can be reprogrammed into a totipotent state through somatic cell nuclear transfer (SCNT). The incomplete reprogramming is the major reason for developmental arrest of SCNT embryos at early stages. In our studies, we found that pathways for autophagy, endocytosis, and apoptosis were incompletely activated in nuclear transfer (NT) 2-cell arrest embryos, whereas extensively inhibited pathways for stem cell pluripotency maintenance, DNA repair, cell cycle, and autophagy may result in NT 4-cell embryos arrest. As for NT normal embryos, a significant shift in expression of developmental transcription factors (TFs) Id1, Pou6f1, Cited1, and Zscan4c was observed. Compared with pluripotent gene Ascl2 being activated only in NT 2-cell, Nanog, Dppa2, and Sall4 had major expression waves in normal development of both NT 2-cell and 4-cell embryos. Additionally, Kdm4b/4d and Kdm5b had been confirmed as key markers in NT 2-cell and 4-cell embryos, respectively. Histone acetylases Kat8, Elp6, and Eid1 were co-activated in NT 2-cell and 4-cell embryos to facilitate normal development. Gadd45a as a key driver functions with Tet1 and Tet2 to improve the efficiency of NT reprogramming. Taken together, our findings provided an important theoretical basis for elucidating the potential molecular mechanisms and identified reprogramming driver factor to improve the efficiency of SCNT reprogramming.
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Affiliation(s)
- Hanshuang Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Mingmin Song
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Wuritu Yang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Pengbo Cao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Lei Zheng
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Yongchun Zuo
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China.
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15
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Li R, Yin YH, Jin J, Liu X, Zhang MY, Yang YE, Qu YQ. Integrative analysis of DNA methylation-driven genes for the prognosis of lung squamous cell carcinoma using MethylMix. Int J Med Sci 2020; 17:773-786. [PMID: 32218699 PMCID: PMC7085273 DOI: 10.7150/ijms.43272] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 02/16/2020] [Indexed: 12/18/2022] Open
Abstract
Background: DNA methylation acts as a key component in epigenetic modifications of genomic function and functions as disease-specific prognostic biomarkers for lung squamous cell carcinoma (LUSC). This present study aimed to identify methylation-driven genes as prognostic biomarkers for LUSC using bioinformatics analysis. Materials and Methods: Differentially expressed RNAs were obtained using the edge R package from 502 LUSC tissues and 49 adjacent non-LUSC tissues. Differentially methylated genes were obtained using the limma R package from 504 LUSC tissues and 69 adjacent non-LUSC tissues. The methylation-driven genes were obtained using the MethylMix R package from 500 LUSC tissues with matched DNA methylation data and gene expression data and 69 non-LUSC tissues with DNA methylation data. Gene ontology and ConsensusPathDB pathway analysis were performed to analyze the functional enrichment of methylation-driven genes. Univariate and multivariate Cox regression analyses were performed to identify the independent effect of differentially methylated genes for predicting the prognosis of LUSC. Results: A total of 44 methylation-driven genes were obtained. Univariate and multivariate Cox regression analyses showed that twelve aberrant methylated genes (ATP6V0CP3, AGGF1P3, RP11-264L1.4, HIST1H4K, LINC01158, CH17-140K24.1, CTC-523E23.14, ADCYAP1, COX11P1, TRIM58, FOXD4L6, CBLN1) were entered into a Cox predictive model associated with overall survival in LUSC patients. Methylation and gene expression combined survival analysis showed that the survival rate of hypermethylation and low-expression of DQX1 and WDR61 were low. The expression of DQX1 had a significantly negatively correlated with the methylation site cg02034222. Conclusion: Methylation-driven genes DQX1 and WDR61 might be potential biomarkers for predicting the prognosis of LUSC.
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Affiliation(s)
- Rui Li
- Department of Respiratory and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Yun-Hong Yin
- Department of Respiratory and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Jia Jin
- Department of Cardiology, Zhangqiu District People's Hospital of Jinan, 250200, Shandong, China
| | - Xiao Liu
- Department of Respiratory and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Meng-Yu Zhang
- Department of Respiratory and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Yi-E Yang
- Department of Clinical Laboratory, Shandong Provincial Qianfoshan Hospital, the First Hospital Affiliated with Shandong First Medical University, Jinan 250014, China
| | - Yi-Qing Qu
- Department of Respiratory and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan 250012, China
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16
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Shi X, Wang B, Chen X, Zheng Y, Ding Y, Wang C. Upregulation of ubiquitin-conjugating enzyme E2Z is associated with human hepatocellular carcinoma. Biochem Biophys Res Commun 2019; 523:25-32. [PMID: 31831168 DOI: 10.1016/j.bbrc.2019.11.170] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 11/25/2019] [Indexed: 12/24/2022]
Abstract
UBE2Z, a member of ubiquitin-conjugating enzymes, has been reported to participate in multiple biological processes. However, its roles in hepatocellular carcinoma (HCC) remain undiscovered. This study aimed at investigating the functions of UBE2Z in HCC. Firstly, we evaluated UBE2Z expression in HCC and identified associations among UBE2Z expression, clinicopathological features, copy number alterations, DNA methylation, and survival of patients using data from the Cancer Genome Atlas (TCGA). As a result, UBE2Z was remarkably overexpressed in HCC tissues relative to normal liver tissues (P < 0.05). High UBE2Z expression was significantly correlated with age, advanced TNM stage, histological grade, vascular invasion, elevated serum alpha-fetoprotein expression (AFP), worse overall survival (OS) and disease-free survival (DFS) of HCC patients (all P < 0.05). Besides, data mining in UCSC Xena Browser showed that UBE2Z DNA amplification which was significantly associated with its expression was common (108 out of 364) in HCC, and that the level of UBE2Z DNA methylation was negatively associated with its expression (Pearson's correlation = -0.4, P < 0.0001). After analyzing the datasets from TCGA, we further confirmed the up-regulation of UBE2Z in 60 HCC tissues and several HCC cell lines. Finally, functional assays were performed and showed that knockdown UBE2Z using small interfering RNA (siRNA) could significantly restrain tumor cell proliferation and suppress cell migration and cell invasion through repressing the expression of MMP2 and MMP9. Meanwhile, UBE2Z knockdown could effectively reduce the expression of p-ERK, p-p38, p-JNK, p-Stat3 and p-JAK2, suggesting that UBE2Z might promote HCC progression by targeting ERK and stat3 signaling pathway. These findings implied that UBE2Z might be considered as a prognostic biomarker in HCC and provided a potential therapeutic tumor-associated antigen for HCC.
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Affiliation(s)
- Xiaokang Shi
- Department of Hepatobiliary Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China; Department of Pathology and Pathophysiology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China
| | - Bin Wang
- Department of Hepatobiliary Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Xiaoyan Chen
- Department of Hepatobiliary Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Yuyang Zheng
- Department of Pathology and Pathophysiology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China
| | - Youming Ding
- Department of Hepatobiliary Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
| | - Changhua Wang
- Department of Pathology and Pathophysiology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China.
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17
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Li R, Yang YE, Yin YH, Zhang MY, Li H, Qu YQ. Methylation and transcriptome analysis reveal lung adenocarcinoma-specific diagnostic biomarkers. J Transl Med 2019; 17:324. [PMID: 31558162 PMCID: PMC6764142 DOI: 10.1186/s12967-019-2068-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 09/14/2019] [Indexed: 02/07/2023] Open
Abstract
Background DNA methylation can regulate the role of long noncoding RNAs (lncRNAs) in the development of lung adenocarcinoma (LUAD). The present study aimed to identify methylation-driven lncRNAs and mRNAs as biomarkers in the prognosis of LUAD using bioinformatics analysis. Methods Differentially expressed RNAs were obtained using the edge R package from 535 LUAD tissues and 59 adjacent non-LUAD tissues. Differentially methylated genes were obtained using the limma R package from 475 LUAD tissues and 32 adjacent non-LUAD tissues. Methylation-driven mRNA and lncRNA were obtained using the MethylMix R package from 465 LUAD tissues with matched DNA methylation and RNA expression and 32 non-LUAD tissues with DNA methylation. Gene ontology and ConsensusPathDB pathway analysis were performed to identify functional enrichment of methylation-driven mRNAs. Univariate and multivariate Cox regression analyses were performed to identify the independent effect of each variable for predicting the prognosis of LUAD. Kaplan–Meier curve analysis of DNA methylation and gene expression might provide potential prognostic biomarkers for LUAD patients. Results A total of 99 methylation-driven mRNAs and 17 methylation-driven lncRNAs were obtained. Univariate and multivariate Cox regression analysis showed that 6 lncRNAs (FOXE1, HOXB13-AS1_2, VMO1, HIST1H3F, AJ003147.8, ASXL3) were retrieved to construct a predictive model associated with overall survival in LUAD patients. Combined DNA methylation and gene expression survival analysis revealed that 4 lncRNAs (AC023824.1, AF186192.1, LINC01354 and WASIR2) and 8 mRNAs (S1PR1, CCDC181, F2RL1, EFS, KLHDC9, MPV17L, GKN2, ITPRIPL1) might act as independent biomarkers for the prognosis of LUAD. Conclusions Methylation-driven lncRNA and mRNA contribute to the survival of LUAD, and 4 lncRNAs and 8 mRNAs might be potential biomarkers for the prognosis of LUAD.
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Affiliation(s)
- Rui Li
- Department of Respiratory and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Yi-E Yang
- Department of Clinical Laboratory, Qianfoshan Hospital of Shandong Province, Jinan, 250014, China
| | - Yun-Hong Yin
- Department of Respiratory and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Meng-Yu Zhang
- Department of Respiratory and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Hao Li
- Department of Respiratory and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, 250012, China.
| | - Yi-Qing Qu
- Department of Respiratory and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, 250012, China.
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18
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Ferioli M, Zauli G, Maiorano P, Milani D, Mirandola P, Neri LM. Role of physical exercise in the regulation of epigenetic mechanisms in inflammation, cancer, neurodegenerative diseases, and aging process. J Cell Physiol 2019; 234:14852-14864. [PMID: 30767204 DOI: 10.1002/jcp.28304] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 01/18/2019] [Accepted: 01/24/2019] [Indexed: 01/24/2023]
Abstract
The genetic heritage for decades has been considered to respond only to gene promoters or suppressors, with specific roles for oncogenes or tumor-suppressor genes. Epigenetics is progressively attracting increasing interest because it has demonstrated the capacity of these regulatory processes to regulate the gene expression without modifying gene sequence. Several factors may influence epigenetics, such as lifestyles including food selection. A role for physical exercise is emerging in the epigenetic regulation of gene expression. In this review, we resume physiological and pathological implications of epigenetic modification induced by the physical activity (PA). Inflammation and cancer mechanisms, immune system, central nervous system, and the aging process receive benefits due to PA through epigenetic mechanisms. Thus, the modulation of epigenetic processes by physical exercise positively influences prevention, development, and the course of inflammatory and cancer diseases, as well as neurodegenerative illnesses. This growing field of studies gives rise to a new role for PA as an option in prevention strategies and to integrate pharmacological therapeutic treatments.
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Affiliation(s)
- Martina Ferioli
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Giorgio Zauli
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Patrizia Maiorano
- Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Daniela Milani
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Prisco Mirandola
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Luca M Neri
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
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Wang J, Zhang Q, Zhu Q, Liu C, Nan X, Wang F, Fang L, Liu J, Xie C, Fu S, Song B. Identification of methylation-driven genes related to prognosis in clear-cell renal cell carcinoma. J Cell Physiol 2019; 235:1296-1308. [PMID: 31273792 PMCID: PMC6899764 DOI: 10.1002/jcp.29046] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 06/13/2019] [Indexed: 12/16/2022]
Abstract
With the participation of the existing treatment methods, the prognosis of advanced clear‐cell renal cell carcinoma (ccRCC) is poor. More evidence indicates the presence of methylation in ccRCC cancer cells, but there is a lack of studies on methylation‐driven genes in ccRCC. We analyzed the open data of ccRCC in The Cancer Genome Atlas database to obtain ccRCC‐related methylation‐driven genes, and then carried out pathway enrichment, survival, and joint survival analyses. More important, we deeply explored the correlation between differential methylation sites and the expression of these driving genes. Finally, we screened 29 methylation‐driven genes via MethylMix, of which six were significantly associated with the survival of ccRCC patients. This study demonstrated that the effect of hypermethylation or hypomethylation on prognosis is different, and the level of methylation of key methylation sites is associated with gene expression. We identified methylation‐driven genes independently predicting prognosis in ccRCC, which offers theoretical support in bioinformatics for the study of methylation in ccRCC and a new perspective for the epigenetic study of ccRCC.
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Affiliation(s)
- Jia Wang
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Jinan, China.,Department of Oncology, Zibo Maternal and Child Health Hospital, Zibo, China.,Department of Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Qiujing Zhang
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Jinan, China.,Department of Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Qingqing Zhu
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Jinan, China.,Department of Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Chengxiang Liu
- Department of Oncology, Jinan Jigang Hospital, Jinan, China
| | - Xueli Nan
- Department of Oncology, Wu Di People Hospital, Binzhou, China
| | - Fuxia Wang
- Department of Oncology, YunCheng Conuntry People's Hospital, YunCheng, China
| | - Lihua Fang
- Department of Oncology, Chang Qing District People's Hospital, Jinan, China
| | - Jie Liu
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Chao Xie
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Shuai Fu
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Bao Song
- Basic Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
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