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Li H, Zhou Q, Wu Z, Lu X. Identification of novel key genes associated with uterine corpus endometrial carcinoma progression and prognosis. ANNALS OF TRANSLATIONAL MEDICINE 2023; 11:100. [PMID: 36819577 PMCID: PMC9929804 DOI: 10.21037/atm-22-6461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 01/10/2023] [Indexed: 01/18/2023]
Abstract
Background Uterine corpus endometrial carcinoma (UCEC) is a common malignant cancer type which affects the health of women worldwide. However, its molecular mechanism has not been elucidated. Methods To identify the hub modules and genes in UCEC associated with clinical phenotypes, the RNA sequencing data and clinical data of 543 UCEC samples were obtained from The Cancer Genome Atlas (TCGA) database and then subjected to weighted gene co-expression network analysis (WGCNA). To explore the potential biological function of the hub modules, Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted. Genes differentially expressed in UCEC were screened according to TCGA data using the "gdcDEAnalysis" package in R (The R Foundation for Statistical Computing). After intersecting with hub genes, the shared genes were used for further survival analyses. The relationship between gene expression level and clinical phenotype was analyzed in the TCGA-UCEC cohort in The University of ALabama at Birmingham CANcer data analysis Portal and the Human Protein Atlas. The microarray data set GSE17025 was also analyzed to validate the gene expression profiles. Results There were 19 coexpression modules generated by WGCNA. Among them, 2 modules with 198 hub genes were highly correlated with clinical features (especially histologic grade and clinical stage). Meanwhile, 4,003 differentially expressed genes (DEGs) were screened out, and 164 DEGs overlapped with hub genes. Survival analyses revealed that high expression of GINS4 and low expression of ESR1 showed a trend of poor prognosis. Further analyses demonstrated that both messenger RNA (mRNA) and protein expression profiles of GINS4 and ESR1 were significantly associated with UCEC development and progression in TCGA and GSE17025 cohorts. Conclusions Based on the integrated bioinformatic analyses, our data indicated that GINS4 and ESR1 might serve as potential prognostic markers and targets for UCEC therapy.
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Affiliation(s)
- Haixia Li
- School of Basic Medical Sciences, Guangxi Medical University, Nanning, China;,College of Stomatology, Hospital of Stomatology, Guangxi Key Laboratory of Nanobody Research/Guangxi Nanobody Engineering Research Center, Guangxi Medical University, Nanning, China;,Department of Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Quan Zhou
- Department of Traditional Chinese Medicine, Renmin Hospital, Hubei University of Medicine, Shiyan, China
| | - Zhangying Wu
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Xiaoling Lu
- School of Basic Medical Sciences, Guangxi Medical University, Nanning, China;,College of Stomatology, Hospital of Stomatology, Guangxi Key Laboratory of Nanobody Research/Guangxi Nanobody Engineering Research Center, Guangxi Medical University, Nanning, China
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Wang J, Guo L, Lv C, Zhou M, Wan Y. Developing mRNA signatures as a novel prognostic biomarker predicting high risk multiple myeloma. Front Oncol 2023; 13:1105196. [PMID: 36910651 PMCID: PMC9995860 DOI: 10.3389/fonc.2023.1105196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/08/2023] [Indexed: 02/25/2023] Open
Abstract
Background Multiple myeloma (MM) remains an essentially incurable disease. This study aimed to establish a predictive model for estimating prognosis in newly diagnosed MM based on gene expression profiles. Methods RNA-seq data were downloaded from the Multiple Myeloma Research Foundation (MMRF) CoMMpass Study and the Genotype-Tissue Expression (GTEx) databases. Weighted gene coexpression network analysis (WGCNA) and protein-protein interaction network analysis were performed to identify hub genes. Enrichment analysis was also conducted. Patients were randomly split into training (70%) and validation (30%) datasets to build a prognostic scoring model based on the least absolute shrinkage and selection operator (LASSO). CIBERSORT was applied to estimate the proportion of 22 immune cells in the microenvironment. Drug sensitivity was analyzed using the OncoPredict algorithm. Results A total of 860 newly diagnosed MM samples and 444 normal counterparts were screened as the datasets. WGCNA was applied to analyze the RNA-seq data of 1589 intersecting genes between differentially expressed genes and prognostic genes. The blue module in the PPI networks was analyzed with Cytoscape, and 10 hub genes were identified using the MCODE plug-in. A three-gene (TTK, GINS1, and NCAPG) prognostic model was constructed. This risk model showed remarkable prognostic value. CIBERSORT assessment revealed the risk model to be correlated with activated memory CD4 T cells, M0 macrophages, M1 macrophages, eosinophils, activated dendritic cells, and activated mast cells. Furthermore, based on OncoPredict, high-risk MM patients were sensitive to eight drugs. Conclusions We identified and constructed a three-gene-based prognostic model, which may provide new and in-depth insights into the treatment of MM patients.
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Affiliation(s)
- Jing Wang
- Department of Oncology and Hematology, Yizheng Hospital of Nanjing Drum Tower Hospital Group, Yizheng, China.,Department of Hematology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China.,The Pq Laboratory of BiomeDx/Rx, Department of Biomedical Engineering, Binghamton University, State University of New York (SUNY), Binghamton, NY, United States
| | - Lili Guo
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chenglan Lv
- Department of Hematology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Min Zhou
- Department of Hematology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Yuan Wan
- The Pq Laboratory of BiomeDx/Rx, Department of Biomedical Engineering, Binghamton University, State University of New York (SUNY), Binghamton, NY, United States
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Zhang Y, Hao X, Han G, Lu Y, Chen Z, Zhang L, Wu J, Wang X. E2F1-mediated GINS2 transcriptional activation promotes tumor progression through PI3K/AKT/mTOR pathway in hepatocellular carcinoma. Am J Cancer Res 2022; 12:1707-1726. [PMID: 35530279 PMCID: PMC9077065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/23/2022] [Indexed: 06/14/2023] Open
Abstract
Hepatocellular carcinoma (HCC) has high morbidity and mortality rates. It is therefore imperative to study the underlying mechanism of HCC to identify potential prognostic biomarkers and therapeutic targets. Recently, GINS2 has been identified to be a cancer-promoting gene in different cancer types. Nevertheless, the exact mechanism of GINS2 in HCC remains to be elucidated. To systematically explore the significance of GINS2, we first assessed the relative expression of GINS2 in pan-cancers based on data obtained from the HCCDB, TIMER, and TCGA databases. Then, we explored the clinical significance of GINS2 in HCC through Kaplan-Meier method as well as univariate and multivariate cox regression analysis. Additionally, functional enrichment analysis of GINS2 was done through GO, KEGG, PPI network, and immune cell infiltration analyses. Functional experiments were also conducted to investigate the biological significance of GINS2 in HCC cell lines. Our research revealed that GINS2 is involved in HCC progression and highlighted its potential value as a crucial diagnostic and therapeutic target for HCC.
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Affiliation(s)
- Yao Zhang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical SciencesNanjing 210029, Jiangsu, China
| | - Xiaopei Hao
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical SciencesNanjing 210029, Jiangsu, China
| | - Guoyong Han
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical SciencesNanjing 210029, Jiangsu, China
| | - Yiwei Lu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical SciencesNanjing 210029, Jiangsu, China
| | - Zhiqiang Chen
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical SciencesNanjing 210029, Jiangsu, China
| | - Long Zhang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical SciencesNanjing 210029, Jiangsu, China
| | - Jindao Wu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical SciencesNanjing 210029, Jiangsu, China
- State Key Laboratory of Reproductive Medicine, Nanjing Medical UniversityNanjing, Jiangsu, China
| | - Xuehao Wang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical SciencesNanjing 210029, Jiangsu, China
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Wu C, Zhou Y, Wang M, Dai G, Liu X, Lai L, Tang S. Bioinformatics Analysis Explores Potential Hub Genes in Nonalcoholic Fatty Liver Disease. Front Genet 2021; 12:772487. [PMID: 34777484 PMCID: PMC8586215 DOI: 10.3389/fgene.2021.772487] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/18/2021] [Indexed: 01/14/2023] Open
Abstract
Background: Nonalcoholic fatty liver disease (NAFLD) is now recognized as the most prevalent chronic liver disease worldwide. However, the dysregulated gene expression for NAFLD is still poorly understood. Material and methods: We analyzed two public datasets (GSE48452 and GSE89632) to identify differentially expressed genes (DEGs) in NAFLD. Then, we performed a series of bioinformatics analyses to explore potential hub genes in NAFLD. Results: This study included 26 simple steatosis (SS), 34 nonalcoholic steatohepatitis (NASH), and 13 healthy controls (HC). We observed 6 up- and 19 down-regulated genes in SS, and 13 up- and 19 down-regulated genes in NASH compared with HC. Meanwhile, the overlapping pathways between SS and NASH were PI3K-Akt signaling pathway and pathways in cancer. Then, we screened out 10 hub genes by weighted Gene Co-Expression Network Analysis (WGCNA) and protein-protein interaction (PPI) networks. Eventually, we found that CYP7A1/GINS2/PDLIM3 were associated with the prognosis of hepatocellular carcinoma (HCC) in the TCGA database. Conclusion: Although further validation is still needed, we provide useful and novel information to explore the potential candidate genes for NAFLD prognosis and therapeutic options.
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Affiliation(s)
- Chutian Wu
- Department of Gastroenterology, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Yun Zhou
- Department of Gastroenterology, The First Affiliated Hospital, Jinan University, Guangzhou, China.,Department of Gastroenterology, The First Affiliated Hospital, Gannan Medical University, Ganzhou, China
| | - Min Wang
- Department of Gastroenterology, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Guolin Dai
- Department of Gastroenterology, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Xiongxiu Liu
- Department of Gastroenterology, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Leizhen Lai
- Department of Gastroenterology, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Shaohui Tang
- Department of Gastroenterology, The First Affiliated Hospital, Jinan University, Guangzhou, China
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Liu B, Liu Z, Wang Y, Lian X, Han Z, Cheng X, Zhu Y, Liu R, Zhao Y, Gao Y. Overexpression of GINS4 is associated with poor prognosis and survival in glioma patients. Mol Med 2021; 27:117. [PMID: 34556022 PMCID: PMC8461916 DOI: 10.1186/s10020-021-00378-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/11/2021] [Indexed: 12/21/2022] Open
Abstract
Background GINS4, an indispensable component of the GINS complex, is vital for a variety of cancer. However, no known empirical research has focused on exploring relationships between GINS4 and glioma. Thus, this study aims to understand and explain the role of GINS4 in glioma. Method First, we used the data in the CGGA, TCGA, GEO, GEPIA, and HPA databases to explore the expression level of GINS4 in glioma, the correlation between GINS4 expression and the clinical features of glioma, its impact on the survival of glioma patients, and verified the analysis results through RT-qPCR, IHC, and meta-analysis. Subsequently, GSEA enrichment analysis is used to find the potential molecular mechanism of GINS4 to promote the malignant process of glioma and the anti-glioma drugs that may target GINS4 screened by CMap analysis. Moreover, we further explored the influence of the GINS4 expression on the immune microenvironment of glioma patients through the TIMER database. Results Our results suggested that GINS4 was elevated in glioma, and the overexpression of GINS4 was connected with a vast number of clinical features. The next, GINS4 as an independent prognostic factor, which can result in an unfavorable prognosis of glioma. Once more, GINS4 may be participating in the oncogenesis of glioma through JAK-STAT signaling pathways, etc. 6-thioguanine, Doxazosin, and Emetine had potential value in the clinical application of drugs targeting GINS4. Finally, the expression exhibited a close relationship with some immune cells, especially Dendritic cells. Conclusion GINS4 is an independent prognostic factor that led to a poor prognosis of glioma. The present study revealed the probable underlying molecular mechanisms of GINS4 in glioma and provided a potential target for improving the prognosis of glioma. Supplementary Information The online version contains supplementary material available at 10.1186/s10020-021-00378-0.
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Affiliation(s)
- Binfeng Liu
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Henan, 450003, Zhengzhou, China
| | - Zhendong Liu
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People's Hospital, Henan International Joint Laboratory of Intelligentized Orthopedics Innovation and Transformation, Henan Key Laboratory for Intelligent Precision Orthopedics, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Henan, 450003, Zhengzhou, China
| | - Yanbiao Wang
- Department of Orthopedics, First Affiliated Hospital of Xinxiang Medical College, Xinjiang, China
| | - Xiaoyu Lian
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Henan, 450003, Zhengzhou, China
| | - Zhibin Han
- Department of Neurosurgery of the First Affiliate Hospital of Harbin Medical University, Harbin, China
| | - Xingbo Cheng
- Department of Neurosurgery of the First Affiliate Hospital of Harbin Medical University, Harbin, China
| | - Yongjie Zhu
- Department of Surgery of Spine and Spinal Cord, Henan University People's Hospital, Henan Provincial People's Hospital, Henan, 450003, Zhengzhou, China
| | - Runze Liu
- Department of Surgery of Spine and Spinal Cord, Henan University People's Hospital, Henan Provincial People's Hospital, Henan, 450003, Zhengzhou, China
| | - Yaoye Zhao
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Henan, 450003, Zhengzhou, China
| | - Yanzheng Gao
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People's Hospital, Henan International Joint Laboratory of Intelligentized Orthopedics Innovation and Transformation, Henan Key Laboratory for Intelligent Precision Orthopedics, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Henan, 450003, Zhengzhou, China.
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Li M, Shi M, Hu C, Chen B, Li S. MALAT1 modulated FOXP3 ubiquitination then affected GINS1 transcription and drived NSCLC proliferation. Oncogene 2021; 40:3870-3884. [PMID: 33972684 DOI: 10.1038/s41388-021-01816-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 04/01/2021] [Accepted: 04/23/2021] [Indexed: 12/22/2022]
Abstract
An increasing number of studies have shown that long-noncoding RNAs (lncRNAs) are involved in the post-translational modifications (PTMs) of protein in a variety of tumors. However, little is known about the exact regulation mechanism of lncRNAs in regulating PTMs in non-small-cell lung carcinoma (NSCLC) proliferation. Metastasis-associated lung adenocarcinoma transcript1 (MALAT1) and GINS complex subunit 1(GINS1) both were upregulated and promoted proliferation progression in NSCLC. In this study, the clinicopathologic significance of MALAT1 and GINS1 in NSCLC was investigated, a positive correlation in their expression was found. The silencing of MALAT1 decreased GINS1 expression and inhibited NSCLC proliferation in vitro and in vivo. The upregulation of GINS1 reversed NSCLC proliferation inhibited by MALAT1 knockdown. FOXP3 (forkhead box protein 3) was identified as the critical transcription factor for GINS1 transcription. In addition, MALAT1 could stabilize FOXP3 by binding to zinc finger (ZF) domain and leucine zipper (LZ) domain of FOXP3. Interestingly, these two domains were also interaction domains for FOXP3 binding with E3 ligase STUB1 (STIP1 homology and U-box containing protein 1). In this way, MALAT1 masked the protein-interacting domain, and inhibited FOXP3 ubiquitination by STUB1. Together, our results identified a novel regulatory axis of MALAT1-FOXP3-GINS1, and demonstrated that MALAT1 played an important modulatory role in PTM of FOXP3 which affects GINS1 transcription and drives proliferation character in NSCLC.
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Affiliation(s)
- Ming Li
- Key Laboratory of Developmental Genes and Human Disease in Ministry of Education, Department of Biochemistry and Molecular Biology, Medical School of Southeast University, Nanjing, China
| | - Minke Shi
- Department of Thoracic and Cardiovascular Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Chaoyue Hu
- Department of Thoracic and Cardiovascular Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Baojun Chen
- Department of Thoracic and Cardiovascular Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Shufeng Li
- Key Laboratory of Developmental Genes and Human Disease in Ministry of Education, Department of Biochemistry and Molecular Biology, Medical School of Southeast University, Nanjing, China.
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Gözen D, Kahraman DC, Narci K, Shehwana H, Konu Ö, Çetin-Atalay R. Transcriptome profiles associated with selenium-deficiency-dependent oxidative stress identify potential diagnostic and therapeutic targets in liver cancer cells. ACTA ACUST UNITED AC 2021; 45:149-161. [PMID: 33907497 PMCID: PMC8068766 DOI: 10.3906/biy-2009-56] [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: 10/06/2020] [Accepted: 02/01/2021] [Indexed: 12/09/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the most common cancer types with high mortality rates and displays increased resistance to various stress conditions such as oxidative stress. Conventional therapies have low efficacies due to resistance and off-target effects in HCC. Here we aimed to analyze oxidative stress-related gene expression profiles of HCC cells and identify genes that could be crucial for novel diagnostic and therapeutic strategies. To identify important genes that cause resistance to reactive oxygen species (ROS), a model of oxidative stress upon selenium (Se) deficiency was utilized. The results of transcriptome-wide gene expression data were analyzed in which the differentially expressed genes (DEGs) were identified between HCC cell lines that are either resistant or sensitive to Se-deficiency-dependent oxidative stress. These DEGs were further investigated for their importance in oxidative stress resistance by network analysis methods, and 27 genes were defined to have key roles; 16 of which were previously shown to have impact on liver cancer patient survival. These genes might have Se-deficiency-dependent roles in hepatocarcinogenesis and could be further exploited for their potentials as novel targets for diagnostic and therapeutic approaches.
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Affiliation(s)
- Damla Gözen
- Cancer Systems Biology Laboratory, Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara Turkey
| | - Deniz Cansen Kahraman
- Cancer Systems Biology Laboratory, Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara Turkey
| | - Kübra Narci
- Cancer Systems Biology Laboratory, Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara Turkey
| | - Huma Shehwana
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi Pakistan
| | - Özlen Konu
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara Turkey
| | - Rengül Çetin-Atalay
- Cancer Systems Biology Laboratory, Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara Turkey
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Qin L, Zhan Z, Wei C, Li X, Zhang T, Li J. Hsa‑circRNA‑G004213 promotes cisplatin sensitivity by regulating miR‑513b‑5p/PRPF39 in liver cancer. Mol Med Rep 2021; 23:421. [PMID: 33864660 PMCID: PMC8025462 DOI: 10.3892/mmr.2021.12060] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 03/01/2021] [Indexed: 02/06/2023] Open
Abstract
In recent years, increasing evidence has confirmed that exosomal circular RNAs (circRNAs) serve a crucial role in the prognostic prediction and diagnosis of liver cancer (LC). The present study compared the expression patterns of exosomal circRNAs during transarterial chemoembolization (TACE). CircRNA sequencing analysis identified 390 differentially expressed circRNAs between the prior TACE and following the first TACE operation groups and 489 differentially expressed circRNAs between the prior to TACE and following the second TACE operation groups. Gene Ontology analysis of the differentially expressed circRNAs demonstrated that they were associated with fatty acid metabolism, receptor binding and membrane protein complexes. Kyoto Encyclopedia of Genes and Genomes pathway analysis predicted that protein digestion and absorption pathways were activated following TACE. A novel gene was screened out; hsa‑circRNA‑G004213 (circ‑G004213) was significantly upregulated following TACE (fold change >10, P < 0.01). Further analysis found circ‑G004213 significantly increased the cisplatin sensitivity of HepG2 cells and positively associated with the prognosis of tumor‑bearing mice. Based on the potential downstream miRNAs and mRNAs, the circRNA‑miRNA‑mRNA network was constructed. It was demonstrated that circ‑G004213 regulated cisplatin resistance via the miR‑513b‑5p/PRPF39 axis. Finally, the present study confirmed that circ‑G004213 was positively associated with the prognosis of patients with LC following TACE. Therefore, circ‑G004213 may be used as an indicator for predicting the efficacy of TACE.
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Affiliation(s)
- Ling Qin
- Department of Gastroenterology, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan 610000, P.R. China
| | - Zibo Zhan
- Department of Gastroenterology, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan 610000, P.R. China
| | - Chunxue Wei
- Department of Gastroenterology, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan 610000, P.R. China
| | - Xuemei Li
- Department of Gastroenterology, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan 610000, P.R. China
| | - Tongqin Zhang
- Department of Gastroenterology, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan 610000, P.R. China
| | - Jun Li
- Department of Gastroenterology, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan 610000, P.R. China
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Epigenetic Mechanisms Are Involved in the Oncogenic Properties of ZNF518B in Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13061433. [PMID: 33801071 PMCID: PMC8004037 DOI: 10.3390/cancers13061433] [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: 02/17/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary The ZNF518B gene, which is up-regulated in colorectal cancer, plays a role in metastasis, but neither the mechanisms involved in this process nor the role of the different isoforms of the gene are known. Here we show that the ratio of these isoforms is related to the relapsing of the disease, and that the protein ZNF518B interacts with enzymes able to introduce epigenetic changes, which may affect the activity of many genes. We also report a list of genes affected in common by ZNF518B and by two of those related enzymes, namely, G9A and EZH2. An in-depth analysis of five of those genes revealed that ZNF518B is involved in the recruitment of the enzymes and in the deposition of the corresponding epigenetic marks. The results highlight the relevance of epigenetic changes in cancer development, and open the possibility of developing therapeutic approaches, as the introduction of epigenetic modifications is reversible. Abstract The ZNF518B gene, which is up-regulated in colorectal cancer, plays a role in cell dissemination and metastasis. It encodes a zinc-finger protein, which interacts with histone methyltransferases G9A and EZH2. The expression of the two major mRNA isoforms 1 (coding for the full protein) and 2 was quantified by RT-qPCR in a cohort of 66 patients. The effects of silencing ZNF518B on the transcriptome of DLD1 and HCT116 cells were analysed by Clariom-S assays and validated by RT-qPCR. The recruitment of methyltransferases and the presence of H3K27me3 were studied by chromatin immunoprecipitation (ChIP). The ratio (isoform 2)/(isoform 1) negatively correlated with the relapsing of disease. The study of the transcriptome of DLD1 and HCT116 cells revealed that many genes affected by silencing ZNF518B are related to cancer. After crossing these results with the list of genes affected by silencing the histone methyltransferases (retrieved in silico), five genes were selected. ChIP analysis revealed that the recruitment of EZH2 is ZNF518B-dependent in KAT2B, RGS4 and EFNA5; the level of H3K27me3 changes in accordance. G9A also binds RGS4 and PADI3 in a ZNF518B-dependent manner. The results highlight the importance of epigenetics in cancer and open a novel therapeutic possibility, as inhibition of histone methyltransferases may reverse the disease-linked histone marks.
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Li H, Cao Y, Ma J, Luo L, Ma B. Expression and prognosis analysis of GINS subunits in human breast cancer. Medicine (Baltimore) 2021; 100:e24827. [PMID: 33725952 PMCID: PMC7982226 DOI: 10.1097/md.0000000000024827] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 01/26/2021] [Accepted: 01/26/2021] [Indexed: 01/05/2023] Open
Abstract
ABSTRACT GINS subunits, a protein complex composed of GINS1, GINS2, GINS3 and GINS4 in the human genome and the expression level of each GINS subunits plays an important role in different human cancers. As one of the most common malignancies after lung cancer in the world, precise biomarkers for early diagnosis and treatment in breast cancer are important. The purpose of our study was to elucidate the expression and prognostic value of GINS subunits in breast cancer.The purpose of present study was to explore the expression level of GINS subunits in breast cancer patients.In the present study, we investigated the gene alteration, gene expression and potential prognostic value of GINS subunits by using the Gene Expression Profiling Interactive Analysis (GEPIA), UALCAN, cBioPortal, and bc-GenExMiner databases. Then, the GeneMANIA database was used to show the genes that associated with GINS subunits. Furthermore, gene ontology pathway analysis was conducted by using the Metascape database. Finally, immune infiltration analysis in GINS subunits were evaluated using the Tumor Immune Estimation Resource (TIMER) database.Our analyses demonstrated that the expression levels of different GINS subunits were different between breast cancer and normal breast tissues. The expression levels of GINS1, GINS2, and GINS4 were significantly higher in breast cancer tissues than in normal tissues. Survival analysis revealed that increased the expression levels of GINS subunits were associated with poor prognoses in all patients with breast cancer. Gene ontology pathway enrichment analysis of the GINS subunits suggested that GINS subunits involved in pathways including the cell cycle checkpoint, DNA replication and other meaningful signaling pathways.We systemically analyzed the expression, prognostic, clinicopathologic values, and potential functional networks of GINS subunits in breast cancer. Our findings showed that individual GINS subunits could be new potential prognostic biomarkers for breast cancer. However, further verification studies are still needed to prove the clinical value of GINS subunits in breast cancer patients.
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Affiliation(s)
- Hongtao Li
- Department of Breast, Head and Neck Surgery
| | - Yanzhen Cao
- Department of Pathology, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Jing Ma
- Department of Breast, Head and Neck Surgery
| | - Lin Luo
- Department of Breast, Head and Neck Surgery
| | - Binlin Ma
- Department of Breast, Head and Neck Surgery
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Bu F, Zhu X, Yi X, Luo C, Lin K, Zhu J, Hu C, Liu Z, Zhao J, Huang C, Zhang W, Huang J. Expression Profile of GINS Complex Predicts the Prognosis of Pancreatic Cancer Patients. Onco Targets Ther 2020; 13:11433-11444. [PMID: 33192076 PMCID: PMC7654543 DOI: 10.2147/ott.s275649] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 09/30/2020] [Indexed: 12/11/2022] Open
Abstract
Background The GINS complex has been implicated in the prognosis of various cancers. It comprises four subunits, encoded by GINS1, GINS2, GINS3, and GINS4 genes. Based on the current understanding, no report exists on the role of the GINS complex in pancreatic cancer. Methods We employed various bioinformatics databases including GEPIA, UALCAN, GEPIA2, and Kaplan Meier Plotter to identify the expression profile of the four genes (GINS1, GINS2, GINS3, and GINS4), their correlation with pancreatic cancer grade as well as their prognostic value of in pancreatic cancer. Western blotting and qRT-PCR analyses were conducted to verify the expression profiles of the four genes in pancreatic cancer. CCK8 and EdU cell experiments were conducted to reveal the role played by the four genes in pancreatic cancer cell proliferation. Results Based on GEPIA, Western blotting, and qRT-PCR analyses, all the four genes in the GINS complex were overexpressed in pancreatic cancer. Notably, the expression of each member was significantly associated with pancreatic cancer grade. The prognostic analysis revealed that not only the whole GINS complex but also each individual were prognostic biomarkers for pancreatic cancer. CCK8 and EdU experiments demonstrated that inhibition of the expression of each GINS member lowered pancreatic cancer cell proliferation. Conclusion This work implicated GINS1, GINS2, GINS3, and GINS4 genes as critical prognostic markers for pancreatic cancer.
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Affiliation(s)
- Fanqin Bu
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province 330006, People's Republic of China.,Jiangxi Medical College of Nanchang University, Nanchang, People's Republic of China
| | - Xiaojian Zhu
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, People's Republic of China
| | - Xuan Yi
- Jiangxi Medical College of Nanchang University, Nanchang, People's Republic of China.,Department of Orthopedics, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province 330006, People's Republic of China
| | - Chen Luo
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province 330006, People's Republic of China.,Jiangxi Medical College of Nanchang University, Nanchang, People's Republic of China
| | - Kang Lin
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province 330006, People's Republic of China.,Jiangxi Medical College of Nanchang University, Nanchang, People's Republic of China
| | - Jinfeng Zhu
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province 330006, People's Republic of China.,Jiangxi Medical College of Nanchang University, Nanchang, People's Republic of China
| | - Cegui Hu
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province 330006, People's Republic of China.,Jiangxi Medical College of Nanchang University, Nanchang, People's Republic of China
| | - Zitao Liu
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province 330006, People's Republic of China.,Jiangxi Medical College of Nanchang University, Nanchang, People's Republic of China
| | - Jiefeng Zhao
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province 330006, People's Republic of China.,Jiangxi Medical College of Nanchang University, Nanchang, People's Republic of China
| | - Chao Huang
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province 330006, People's Republic of China.,Jiangxi Medical College of Nanchang University, Nanchang, People's Republic of China
| | - Wenjun Zhang
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province 330006, People's Republic of China.,Jiangxi Medical College of Nanchang University, Nanchang, People's Republic of China
| | - Jun Huang
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province 330006, People's Republic of China
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12
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APC CDC20-mediated degradation of PHD3 stabilizes HIF-1a and promotes tumorigenesis in hepatocellular carcinoma. Cancer Lett 2020; 496:144-155. [PMID: 33039559 DOI: 10.1016/j.canlet.2020.10.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/10/2020] [Accepted: 10/06/2020] [Indexed: 01/04/2023]
Abstract
CDC20 regulates cell cycle progression by targeting key substrates for destruction, but its role in hepatocellular carcinoma (HCC) tumorigenesis remains to be explored. Here, by using weighted gene co-expression network analysis (WGCNA), we identified CDC20 as a hub gene in HCC. We demonstrated that CDC20 expression is correlated with HIF-1 activity and overall survival (OS) of clinic HCC patients. The activity of HIF-1 is regulated by the stability of HIF-1a subunit, which is hydroxylated by oxygen-dependent prolyl hydroxylase enzymes, the PHDs. In addition, we show that genetic ablation or pharmacological inhibition of CDC20 can accelerate the degradation of HIF-1a and impair VEGF secretion in HCC cells. Mechanistically, we found that CDC20 binds to the destruction-box (D-box) motif present in the PHD3 protein to promote its polyubiquitination and degradation. The depletion of endogenous PHD3 in CDC20 knockdown HCC cells greatly attenuated the decline of HIF-1a protein and restored the secretion of VEGF. In contrast, overexpression of a non-degradable PHD3 mutant significantly inhibited the proliferation of HCC cells both in vitro and in vivo. Collectively, our findings indicate that CDC20 plays a crucial role in the development of HCC by governing PHD3 protein.
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13
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Zhang D, Liu J, Xie T, Jiang Q, Ding L, Zhu J, Ye Q. Oleate acid-stimulated HMMR expression by CEBPα is associated with nonalcoholic steatohepatitis and hepatocellular carcinoma. Int J Biol Sci 2020; 16:2812-2827. [PMID: 33061798 PMCID: PMC7545721 DOI: 10.7150/ijbs.49785] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/11/2020] [Indexed: 02/06/2023] Open
Abstract
Non-alcoholic steatohepatitis (NASH) is a type of nonalcoholic fatty liver disease and has become a major risk factor for hepatocellular carcinoma (HCC). However, the underlying pathophysiological mechanisms are still elusive. Here, we identify hyaluronan-mediated motility receptor (HMMR) as a critical gene associated with NASH/HCC by combination of bioinformatic analysis and functional experiments. Analysis of differentially expressed genes (DEGs) between normal controls and NASH/HCC identified 5 hub genes (HMMR, UBE2T, TYMS, PTTG1 and GINS2). Based on the common DEGs, analyses of univariate and multivariate Cox regression and the area under the curve (AUC) value of the receiver operating characteristic (ROC) indicate that HMMR is the most significant gene associated with NASH/HCC among five hub genes. Oleate acid (OA), one of fatty acids that induce cellular adipogenesis, stimulates HMMR expression via CCAAT/enhancer-binding protein α (CEBPα). CEBPα increases the expression of HMMR through binding to its promoter. HMMR promotes HCC cell proliferation in vitro via activation of G1/S and G2/M checkpoint transitions, concomitant with a marked increase of the positive cell cycle regulators, including cyclin D1, cyclin E, and cyclin B1. Knockdown of HMMR suppresses HCC tumor growth in nude mice. Our study identifies an important role of HMMR in NASH/HCC, and suggests that HMMR may be a useful target for therapy and prognostic prediction of NASH/HCC patients.
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Affiliation(s)
- Deyu Zhang
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing 100850, China
| | - Jiahong Liu
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing 100850, China.,Department of Oncology, The Fourth Medical Center, PLA General Hospital, Beijing 100048, China
| | - Tian Xie
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing 100850, China
| | - Qiwei Jiang
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing 100850, China
| | - Lihua Ding
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing 100850, China
| | - Jianhua Zhu
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing 100850, China.,Department of Oncology, The Fourth Medical Center, PLA General Hospital, Beijing 100048, China
| | - Qinong Ye
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing 100850, China
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14
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Yu S, Zhu L, Xie P, Jiang S, Wang K, Liu Y, He J, Ren Y. Mining the prognostic significance of the GINS2 gene in human breast cancer using bioinformatics analysis. Oncol Lett 2020; 20:1300-1310. [PMID: 32724372 PMCID: PMC7377083 DOI: 10.3892/ol.2020.11651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 11/26/2019] [Indexed: 12/24/2022] Open
Abstract
A number of studies have demonstrated the crucial functions of GINS2 within the GINS complex in various types of cancer. However, the molecular mechanisms and prognostic value of GINS2 in breast cancer remain unknown. The present study used; BC-GenExMiner, COSMIC, UCSC Xena, The Human Protein Atlas, GEPIA, cBioPortal, GeneMANIA, TIMER and Oncomine, in order to investigate gene expression, co-expression, clinical parameters and mutations in GINS2 in patients with breast cancer. Furthermore, the present study assessed the prognostic value of GINS2 in patients with breast cancer via the Kaplan-Meier plotter database. The results of the present study demonstrated that the mRNA levels of GINS2 were significantly higher in breast cancer tissue compared with normal tissue. In addition, high mRNA expression levels of GINS2 were associated with high Scarff-Bloom-Richardson status grades, a basal-like status and age (≤51 years); however, it was not associated with lymph node metastasis. The survival analysis revealed that increased GINS2 mRNA levels were associated with a worse prognosis for relapse-free survival in all patients with breast cancer, particularly in those with estrogen receptor-positive and progesterone receptor-positive subtypes. In addition, a positive association between the GINS2, CENPM and MCM4 genes was confirmed. The results of the present study suggest that GINS2 could be used as a potential prognostic biomarker for breast cancer. Nevertheless, further studies are necessary to confirm the effects of GINS2 on the pathogenesis and development of patients with breast cancer.
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Affiliation(s)
- Shibo Yu
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Lizhe Zhu
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Peiling Xie
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Siyuan Jiang
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Ke Wang
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Yang Liu
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Jianjun He
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Yu Ren
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
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MCMs in Cancer: Prognostic Potential and Mechanisms. Anal Cell Pathol (Amst) 2020; 2020:3750294. [PMID: 32089988 PMCID: PMC7023756 DOI: 10.1155/2020/3750294] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/25/2020] [Indexed: 12/17/2022] Open
Abstract
Enabling replicative immortality and uncontrolled cell cycle are hallmarks of cancer cells. Minichromosome maintenance proteins (MCMs) exhibit helicase activity in replication initiation and play vital roles in controlling replication times within a cell cycle. Overexpressed MCMs are detected in various cancerous tissues and cancer cell lines. Previous studies have proposed MCMs as promising proliferation markers in cancers, while the prognostic values remain controversial and the underlying mechanisms remain unascertained. This review provides an overview of the significant findings regarding the cellular and tumorigenic functions of the MCM family. Besides, current evidence of the prognostic roles of MCMs is retrospectively reviewed. This work also offers insight into the mechanisms of MCMs prompting carcinogenesis and adverse prognosis, providing information for future research. Finally, MCMs in liver cancer are specifically discussed, and future perspectives are provided.
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