101
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Xie XP, Xie YF, Wang HQ. A regulation probability model-based meta-analysis of multiple transcriptomics data sets for cancer biomarker identification. BMC Bioinformatics 2017; 18:375. [PMID: 28830341 PMCID: PMC5568075 DOI: 10.1186/s12859-017-1794-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Accepted: 08/15/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Large-scale accumulation of omics data poses a pressing challenge of integrative analysis of multiple data sets in bioinformatics. An open question of such integrative analysis is how to pinpoint consistent but subtle gene activity patterns across studies. Study heterogeneity needs to be addressed carefully for this goal. RESULTS This paper proposes a regulation probability model-based meta-analysis, jGRP, for identifying differentially expressed genes (DEGs). The method integrates multiple transcriptomics data sets in a gene regulatory space instead of in a gene expression space, which makes it easy to capture and manage data heterogeneity across studies from different laboratories or platforms. Specifically, we transform gene expression profiles into a united gene regulation profile across studies by mathematically defining two gene regulation events between two conditions and estimating their occurring probabilities in a sample. Finally, a novel differential expression statistic is established based on the gene regulation profiles, realizing accurate and flexible identification of DEGs in gene regulation space. We evaluated the proposed method on simulation data and real-world cancer datasets and showed the effectiveness and efficiency of jGRP in identifying DEGs identification in the context of meta-analysis. CONCLUSIONS Data heterogeneity largely influences the performance of meta-analysis of DEGs identification. Existing different meta-analysis methods were revealed to exhibit very different degrees of sensitivity to study heterogeneity. The proposed method, jGRP, can be a standalone tool due to its united framework and controllable way to deal with study heterogeneity.
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Affiliation(s)
- Xin-Ping Xie
- School of Mathematics and Physics, Anhui Jianzhu University, Hefei, Anhui 230022 China
| | - Yu-Feng Xie
- School of Mathematics and Physics, Anhui Jianzhu University, Hefei, Anhui 230022 China
- Cancer Hospital, CAS, Hefei, Anhui 230031 China
| | - Hong-Qiang Wang
- Cancer Hospital, CAS, Hefei, Anhui 230031 China
- MICB Lab., Hefei Institutes of Physical Science, CAS, Hefei, 230031 China
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102
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Cdc20: At the Crossroads between Chromosome Segregation and Mitotic Exit. Trends Biochem Sci 2017; 42:193-205. [PMID: 28202332 DOI: 10.1016/j.tibs.2016.12.001] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/13/2016] [Accepted: 12/06/2016] [Indexed: 11/21/2022]
Abstract
Cell-division cycle protein 20 homologue (Cdc20) has important functions in chromosome segregation and mitotic exit. Cdc20 is the target of the spindle assembly checkpoint (SAC) and a key cofactor of the anaphase-promoting complex or cyclosome (APC/C) E3 ubiquitin ligase, thus regulating APC/C ubiquitin activity on specific substrates for their subsequent degradation by the proteasome. Here we discuss the roles of Cdc20 in SAC signalling and mitotic exit, describe how the integration of traditional approaches with emerging technologies has revealed new details of Cdc20 functions, comment about the potential of Cdc20 as a therapeutic target for the treatment of human malignancies, and discuss recent advances and controversies in the mechanistic understanding of the control of chromosome segregation during cell division.
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103
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Inhibition of Cell Survival by Curcumin Is Associated with Downregulation of Cell Division Cycle 20 (Cdc20) in Pancreatic Cancer Cells. Nutrients 2017; 9:nu9020109. [PMID: 28165402 PMCID: PMC5331540 DOI: 10.3390/nu9020109] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 01/19/2017] [Accepted: 01/25/2017] [Indexed: 01/23/2023] Open
Abstract
Pancreatic cancer is one of the most aggressive human tumors in the United States. Curcumin, a polyphenol derived from the Curcuma longa plant, has been reported to exert its antitumor activity in pancreatic cancer. However, the molecular mechanisms of curcumin-mediated tumor suppressive function have not been fully elucidated. In the current study, we explore whether curcumin exhibits its anti-cancer function through inhibition of oncoprotein cell division cycle 20 (Cdc20) in pancreatic cancer cells. We found that curcumin inhibited cell growth, enhanced apoptosis, induced cell cycle arrest and retarded cell invasion in pancreatic cancer cells. Moreover, we observed that curcumin significantly inhibited the expression of Cdc20 in pancreatic cancer cells. Furthermore, our results demonstrated that overexpression of Cdc20 enhanced cell proliferation and invasion, and abrogated the cytotoxic effects induced by curcumin in pancreatic cancer cells. Consistently, downregulation of Cdc20 promoted curcumin-mediated anti-tumor activity. Therefore, our findings indicated that inhibition of Cdc20 by curcumin could be useful for the treatment of pancreatic cancer patients.
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104
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Li H, Jiang X, Zhu S, Sui L. Identification of personalized dysregulated pathways in hepatocellular carcinoma. Pathol Res Pract 2017; 213:327-332. [PMID: 28215647 DOI: 10.1016/j.prp.2017.01.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 01/11/2017] [Accepted: 01/19/2017] [Indexed: 11/27/2022]
Abstract
INTRODUCTION Hepatocellular carcinoma (HCC) is the most common liver malignancy, and ranks the fifth most prevalent malignant tumors worldwide. In general, HCC are detected until the disease is at an advanced stage and may miss the best chance for treatment. Thus, elucidating the molecular mechanisms is critical to clinical diagnosis and treatment for HCC. The purpose of this study was to identify dysregulated pathways of great potential functional relevance in the progression of HCC. MATERIALS AND METHODS Microarray data of 72 pairs of tumor and matched non-tumor surrounding tissues of HCC were transformed to gene expression data. Differentially expressed genes (DEG) between patients and normal controls were identified using Linear Models for Microarray Analysis. Personalized dysregulated pathways were identified using individualized pathway aberrance score module. RESULTS 169 differentially expressed genes (DEG) were obtained with |logFC|≥1.5 and P≤0.01. 749 dysregulated pathways were obtained with P≤0.01 in pathway statistics, and there were 93 DEG overlapped in the dysregulated pathways. After performing normal distribution analysis, 302 pathways with the aberrance probability≥0.5 were identified. By ranking pathway with aberrance probability, the top 20 pathways were obtained. Only three DEGs (TUBA1C, TPR, CDC20) were involved in the top 20 pathways. CONCLUSION These personalized dysregulated pathways and overlapped genes may give new insights into the underlying biological mechanisms in the progression of HCC. Particular attention can be focused on them for further research.
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Affiliation(s)
- Hong Li
- Department of Oncology, Weihai Central Hospital, Weihai, 264400, Shandong, PR China
| | - Xiumei Jiang
- Department of Oncology, Weihai Central Hospital, Weihai, 264400, Shandong, PR China
| | - Shengjie Zhu
- Department of Oncology, Weihai Central Hospital, Weihai, 264400, Shandong, PR China
| | - Lihong Sui
- Department of Oncology, Weihai Central Hospital, Weihai, 264400, Shandong, PR China.
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105
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Zhang M, Yao F, Luan H, Zhao W, Jing T, Zhang S, Hou L, Zou X. APC/C CDC20 and APC/C play pivotal roles in the process of embryonic development in Artemia sinica. Sci Rep 2016; 6:39047. [PMID: 27991546 PMCID: PMC5171921 DOI: 10.1038/srep39047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 11/17/2016] [Indexed: 11/09/2022] Open
Abstract
Anaphase Promoting Complex or Cyclosome (APC/C) is a representative E3 ubiquitin ligase, triggering the transition of metaphase to anaphase by regulating degradation and ensures the exit from mitosis. Cell division cycle 20 (CDC20) and Cell division cycle 20 related protein 1 (CDH1), as co-activators of APC/C, play significant roles in the spindle assembly checkpoint, guiding ubiquitin-mediated degradation, together with CDC23. During the embryonic development of the brine shrimp, Artemia sinica, CDC20, CDH1 and CDC23 participate in cell cycle regulation, but the specific mechanisms of their activities remain unknown. Herein, the full-length cDNAs of cdc20 and cdc23 from A. sinica were cloned. Real-time PCR analyzed the expression levels of As-cdc20 and As-cdc23. The locations of CDH1, CDC20 and CDC23 showed no tissue or organ specificity. Furthermore, western blotting showed that the levels of As-CDC20, securin, cyclin B, CDK1, CDH1, CDC14B, CDC23 and geminin proteins conformed to their complicated degradation relationships during different embryo stages. Our research revealed that As-CDC20, As-CDH1 and APC mediate the mitotic progression, downstream proteins degradation and cellular differentiation in the process of embryonic development in A. sinica.
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Affiliation(s)
- Mengchen Zhang
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China
| | - Feng Yao
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China
| | - Hong Luan
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China
| | - Wei Zhao
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China
| | - Ting Jing
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China
| | - Shuang Zhang
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China
| | - Lin Hou
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China
| | - Xiangyang Zou
- Department of Biology, Dalian Medical University, Dalian 116044, China
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106
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Li K, Mao Y, Lu L, Hu C, Wang D, Si-Tu J, Lu M, Peng S, Qiu J, Gao X. Silencing of CDC20 suppresses metastatic castration-resistant prostate cancer growth and enhances chemosensitivity to docetaxel. Int J Oncol 2016; 49:1679-85. [DOI: 10.3892/ijo.2016.3671] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 07/26/2016] [Indexed: 11/06/2022] Open
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107
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Choudhary D, Pandey A, Adhikary S, Ahmad N, Bhatia C, Bhambhani S, Trivedi PK, Trivedi R. Genetically engineered flavonol enriched tomato fruit modulates chondrogenesis to increase bone length in growing animals. Sci Rep 2016; 6:21668. [PMID: 26917158 PMCID: PMC4768317 DOI: 10.1038/srep21668] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 01/26/2016] [Indexed: 11/19/2022] Open
Abstract
Externally visible body and longitudinal bone growth is a result of proliferation of chondrocytes. In growth disorder, there is delay in the age associated increase in height. The present study evaluates the effect of extract from transgenic tomato fruit expressing AtMYB12 transcription factor on bone health including longitudinal growth. Constitutive expression of AtMYB12 in tomato led to a significantly enhanced biosynthesis of flavonoids in general and the flavonol biosynthesis in particular. Pre-pubertal ovary intact BALB/c mice received daily oral administration of vehicle and ethanolic extract of wild type (WT-TOM) and transgenic AtMYB12-tomato (MYB12-TOM) fruits for six weeks. Animal fed with MYB12-TOM showed no inflammation in hepatic tissues and normal sinusoidal Kupffer cell morphology. MYB12-TOM extract significantly increased tibial and femoral growth and subsequently improved the bone length as compared to vehicle and WT-TOM. Histomorphometry exhibited significantly wider distal femoral and proximal tibial growth plate, increased number and size of hypertrophic chondrocytes in MYB12-TOM which corroborated with micro-CT and expression of BMP-2 and COL-10, marker genes for hypertrophic cells. We conclude that metabolic reprogramming of tomato by AtMYB12 has the potential to improve longitudinal bone growth thus helping in achievement of greater peak bone mass during adolescence.
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Affiliation(s)
- Dharmendra Choudhary
- CSIR-Central Drug Research Institute (CSIR-CDRI), Endocrinology Division, Jankipuram Extension, Sitapur Road, Lucknow-226031, INDIA
| | - Ashutosh Pandey
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow-226 001, INDIA
| | - Sulekha Adhikary
- CSIR-Central Drug Research Institute (CSIR-CDRI), Endocrinology Division, Jankipuram Extension, Sitapur Road, Lucknow-226031, INDIA
| | - Naseer Ahmad
- CSIR-Central Drug Research Institute (CSIR-CDRI), Endocrinology Division, Jankipuram Extension, Sitapur Road, Lucknow-226031, INDIA
| | - Chitra Bhatia
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow-226 001, INDIA
| | - Sweta Bhambhani
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow-226 001, INDIA
| | - Prabodh Kumar Trivedi
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow-226 001, INDIA
| | - Ritu Trivedi
- CSIR-Central Drug Research Institute (CSIR-CDRI), Endocrinology Division, Jankipuram Extension, Sitapur Road, Lucknow-226031, INDIA
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108
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Gayyed MF, El-Maqsoud NMRA, Tawfiek ER, El Gelany SAA, Rahman MFA. A comprehensive analysis of CDC20 overexpression in common malignant tumors from multiple organs: its correlation with tumor grade and stage. Tumour Biol 2015; 37:749-62. [DOI: 10.1007/s13277-015-3808-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 07/20/2015] [Indexed: 11/29/2022] Open
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109
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Compound 331 selectively induces glioma cell death by upregulating miR-494 and downregulating CDC20. Sci Rep 2015; 5:12003. [PMID: 26153143 PMCID: PMC4495416 DOI: 10.1038/srep12003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 06/12/2015] [Indexed: 12/27/2022] Open
Abstract
Malignant gliomas are the most common malignant tumors in the central nervous system (CNS). Up to date, the prognosis of glioma is still very poor, effective therapy with less side-effect is very necessary. Herein, we identify a compound named as "331" selectively induced cell death in glioma cells but not in astrocytes. Compound 331 upregulated miR-494 and downregulated CDC20 in glioma cells but not in astrocytes. These results suggest that compound 331 could be a potential drug selectively targeting glioma cells through upregulating miR-494 and downregulating CDC20.
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110
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Targeting Cdc20 as a novel cancer therapeutic strategy. Pharmacol Ther 2015; 151:141-51. [PMID: 25850036 DOI: 10.1016/j.pharmthera.2015.04.002] [Citation(s) in RCA: 172] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 03/31/2015] [Indexed: 12/25/2022]
Abstract
The Anaphase Promoting Complex (APC, also called APC/C) regulates cell cycle progression by forming two closely related, but functionally distinct E3 ubiquitin ligase sub-complexes, APC(Cdc20) and APC(Cdh1), respectively. Emerging evidence has begun to reveal that Cdc20 and Cdh1 have opposing functions in tumorigenesis. Specifically, Cdh1 functions largely as a tumor suppressor, whereas Cdc20 exhibits an oncogenic function, suggesting that Cdc20 could be a promising therapeutic target for combating human cancer. However, the exact underlying molecular mechanisms accounting for their differences in tumorigenesis remain largely unknown. Therefore, in this review, we summarize the downstream substrates of Cdc20 and the critical functions of Cdc20 in cell cycle progression, apoptosis, ciliary disassembly and brain development. Moreover, we briefly describe the upstream regulators of Cdc20 and the oncogenic role of Cdc20 in a variety of human malignancies. Furthermore, we summarize multiple pharmacological Cdc20 inhibitors including TAME and Apcin, and their potential clinical benefits. Taken together, development of specific Cdc20 inhibitors could be a novel strategy for the treatment of human cancers with elevated Cdc20 expression.
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