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Liang J, Cui Z, Wu C, Yu Y, Tian R, Xie H, Jin Z, Fan W, Xie W, Huang Z, Xu W, Zhu J, You Z, Guo X, Qiu X, Ye J, Lang B, Li M, Tan S, Hu Z. DeepEBV: A deep learning model to predict Epstein-Barr virus (EBV) integration sites. Bioinformatics 2021; 37:3405-3411. [PMID: 34009299 DOI: 10.1093/bioinformatics/btab388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 03/26/2021] [Accepted: 05/17/2021] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Epstein-Barr virus (EBV) is one of the most prevalent DNA oncogenic viruses. The integration of EBV into the host genome has been reported to play an important role in cancer development. The preference of EBV integration showed strong dependence on the local genomic environment, which enables the prediction of EBV integration sites. RESULTS An attention-based deep learning model, DeepEBV, was developed to predict EBV integration sites by learning local genomic features automatically. First, DeepEBV was trained and tested using the data from the dsVIS database. The results showed that DeepEBV with EBV integration sequences plus Repeat peaks and 2 fold data augmentation performed the best on the training dataset. Furthermore, the performance of the model was validated in an independent dataset. In addition, the motifs of DNA-binding proteins could influence the selection preference of viral insertional mutagenesis. Furthermore, the results showed that DeepEBV can predict EBV integration hotspot genes accurately. In summary, DeepEBV is a robust, accurate and explainable deep learning model, providing novel insights into EBV integration preferences and mechanisms. AVAILABILITY DeepEBV is available as open-source software and can be downloaded from https://github.com/JiuxingLiang/DeepEBV.gitSupplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jiuxing Liang
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, China; Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou 510631, China
| | - Zifeng Cui
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Canbiao Wu
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, China; Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou 510631, China
| | - Yao Yu
- Department of Urology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853 China.,School of Medicine, Nankai University, Tianjin 300071, China
| | - Rui Tian
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Hongxian Xie
- STech Company Bio-X Lab, Zhuhai 519000, Guangdong, China
| | - Zhuang Jin
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Weiwen Fan
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Weiling Xie
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Zhaoyue Huang
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Wei Xu
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Jingjing Zhu
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Zeshan You
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Xiaofang Guo
- Department of Medical Oncology of the Eastern Hospital, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510700, China
| | - Xiaofan Qiu
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, China; Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou 510631, China
| | - Jiahao Ye
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, China; Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou 510631, China.,School of Computer Science, South China Normal University, Guangzhou 510631, China
| | - Bin Lang
- School of Health Sciences and Sports, Macao Polytechnic Institute, China
| | - Mengyuan Li
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Songwei Tan
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zheng Hu
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China.,Department of Obstetrics and Gynaecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
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Chi D, Zhang W, Jia Y, Cong D, Hu S. Spalt-Like Transcription Factor 1 (SALL1) Gene Expression Inhibits Cell Proliferation and Cell Migration of Human Glioma Cells Through the Wnt/β-Catenin Signaling Pathway. Med Sci Monit Basic Res 2019; 25:128-138. [PMID: 31040265 PMCID: PMC6511114 DOI: 10.12659/msmbr.915067] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Background The spalt-like transcription factor 1 (SALL1) gene is a member of the Krüppel-associated box-containing zinc finger proteins (KRAB-ZFPs) and has been shown to modulate the onset and progression of human tumors. This study aimed to investigate the regulatory effects and mechanisms of SALL1 gene expression in human glioblastoma and glioma cells and tissue samples from patients with cerebral glioma. Material/Methods The human glioblastoma cell lines, LN229, U87-MG, U-251, U343, and the Hs683 glioma cell line were studied. The cell counting kit-8 (CCK-8) assay, cell cycle assay, wound-healing assay, transwell assay, Western blot, and quantitative real-time polymerase chain reaction (qRT-PCR) were used to evaluate cell proliferation, cell migration, and the cell cycle and expression of SALL1. Expression of SALL1 mRNA in 120 samples of cerebral glioma and 20 samples of normal brain were studied. Overall survival data from patients with cerebral glioma were analyzed. Results SALL1 expression was down-regulated in human glioblastoma and glioma cells and in cerebral glioma tissues. Down-regulation of SALL1 expression was associated with reduced overall survival. Overexpression of SALL1 was associated with inhibition of cell proliferation associated with cell cycle arrest at the G0/G1 phase. SALL1 inhibited cell migration by preventing epithelial-mesenchymal transition (EMT) and down-regulating the expression of stem cell markers. Reduced levels of β-catenin and downregulation of c-Myc and cyclin D1 and upregulation of p21and p27 expression were associated with SALL1 expression. Conclusions In human glioblastoma cells and cerebral glioma tissues, SALL1 acted as a tumor suppressor gene by inhibiting Wnt/β-catenin signaling.
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Affiliation(s)
- Dapeng Chi
- Department of Neurological Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China (mainland)
| | - Wei Zhang
- Department of Pathology, Shanghai Tenth Peoples' Hospital, Tongji University School of Medicine, Shanghai, China (mainland)
| | - Yulong Jia
- Department of Neurological Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China (mainland)
| | - Damin Cong
- Department of Neurological Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China (mainland)
| | - Shaoshan Hu
- Department of Neurological Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China (mainland)
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Xiang S, Xiang T, Xiao Q, Li Y, Shao B, Luo T. Zinc-finger protein 545 is inactivated due to promoter methylation and functions as a tumor suppressor through the Wnt/β-catenin, PI3K/AKT and MAPK/ERK signaling pathways in colorectal cancer. Int J Oncol 2017; 51:801-811. [PMID: 28677721 PMCID: PMC5564408 DOI: 10.3892/ijo.2017.4064] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/26/2017] [Indexed: 12/31/2022] Open
Abstract
The transcription factor, zinc-finger protein 545 (ZNF545), that belongs to the Kruppel-associated box zinc-finger protein (KRAB-ZFP) family, acts as a tumor suppressor and is inactivated by promoter methylation in cancers such as nasopharyngeal carcinoma, breast cancer, and gastric cancer, but its role in colorectal cancer (CRC) is unknown. The purpose of this study was to characterize the ZNF545 expression, methylation status, biological function, and related molecular mechanisms in CRC. The results showed that ZNF545 was expressed in adult normal colorectal tissues, but downregulated or silenced in CRC cell lines, and this mechanism was reversed by demethylation treatment with 5-aza-2′-deoxycytidine and trichostatin A. The results also showed that the expression of ZNF545 in primary CRC tissues was significantly downregulated compared to adjacent tissues (p<0.05). Overexpression of ZNF545 caused CRC cell cycle arrest and apoptosis, suppressed cell proliferation, and suppressed colony formation and migration in vitro, showing that ZNF545 can function as a tumor suppressor. This function was also shown in nude mice. Furthermore, Wnt/β-catenin, phosphatidylinositol 3 kinase/protein kinase B (PI3K/AKT), and mitogen-activated protein kinases/extracellular signal-regulated kinase (MAPK/ERK) signaling pathways participated in the regulation of ZNF545 in CRC cells. Together, the results suggested that ZNF545 functions as a tumor suppressor in CRC and is frequently inactivated by promoter methylation.
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Affiliation(s)
- Shili Xiang
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Tingxiu Xiang
- Molecular Oncology and Epigenetics Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Qian Xiao
- Department of Breast and Thyroid, The Hospital of Chongqing Traditional Chinese Medicine, Chongqing 400011, P.R. China
| | - Yunhai Li
- Molecular Oncology and Epigenetics Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Bianfei Shao
- Molecular Oncology and Epigenetics Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Tao Luo
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
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Kitajima M, Iwamura C, Miki-Hosokawa T, Shinoda K, Endo Y, Watanabe Y, Shinnakasu R, Hosokawa H, Hashimoto K, Motohashi S, Koseki H, Ohara O, Yamashita M, Nakayama T. Enhanced Th2 cell differentiation and allergen-induced airway inflammation in Zfp35-deficient mice. THE JOURNAL OF IMMUNOLOGY 2009; 183:5388-96. [PMID: 19783676 DOI: 10.4049/jimmunol.0804155] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Studies of human asthma and of animal models of allergic airway inflammation revealed a crucial role for Th2 cells in the pathogenesis of allergic asthma. Kruppel-type zinc finger proteins are the largest family of a regulatory transcription factor for cellular development and function. Zinc finger protein (Zfp) 35 is an 18-zinc finger motif-containing Kruppel-type zinc finger protein, while its function remains largely unknown. The aim of this study was to clarify the role of Zfp35 in the pathogenesis of Th2-dependent allergic inflammation, such as allergic asthma. We examined airway eosinophilic inflammation and hyperresponsiveness in two mouse models, which use our newly generated Zfp35-deficient (Zfp35(-/-)) mice and adoptive transfer of cells. In Zfp35(-/-) mice, Th2 cell differentiation, Th2 cytokine production, eosinophilic inflammation, and airway hyperresponsiveness were substantially enhanced. Furthermore, adoptive transfer of Ag-sensitized Zfp35(-/-) CD4 T cells into the asthmatic mice resulted in enhanced airway inflammation and airway hyperresponsiveness. These results indicate that Zfp35 controls Th2 cell differentiation, allergic airway inflammation, and airway hyperresponsiveness in a negative manner. Thus, Zfp35 may control Th2-dependent diseases, such as allergic asthma.
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Affiliation(s)
- Masayuki Kitajima
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
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Harper J, Yan L, Loureiro RM, Wu I, Fang J, D'Amore PA, Moses MA. Repression of Vascular Endothelial Growth Factor Expression by the Zinc Finger Transcription Factor ZNF24. Cancer Res 2007; 67:8736-41. [PMID: 17875714 DOI: 10.1158/0008-5472.can-07-1617] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Vascular endothelial growth factor (VEGF) is a potent stimulator of angiogenesis. Although many positive regulators of VEGF have been identified, relatively little is known regarding the negative regulation of VEGF expression. We identified a zinc finger transcription factor, ZNF24, that may repress VEGF transcription. An inverse correlation between expression of VEGF and ZNF24 was observed in a series of independent studies. ZNF24 was up-regulated in angiogenic tumor nodules where VEGF expression is significantly decreased compared with preangiogenic nodules. In human breast carcinoma cells cultured under normoxic conditions, ZNF24 levels were significantly up-regulated whereas VEGF levels were low. In contrast, VEGF was significantly increased in hypoxic cells whereas ZNF24 was down-regulated. The same inverse correlation between ZNF24 and VEGF was also observed in 70% of matched cDNA pairs of normal and malignant tissues from human colon and breast biopsies. Overexpression of ZNF24 resulted in a significant down-regulation of VEGF, whereas silencing of ZNF24 with small interfering RNA led to increased VEGF expression. Cotransfection of ZNF24 and a VEGF promoter luciferase reporter construct in MDA-MB-231 cells resulted in a significant decrease in VEGF promoter activity. Taken together, these data suggest that ZNF24 is involved in negative regulation of VEGF and may represent a novel repressor of VEGF transcription.
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Affiliation(s)
- Jay Harper
- Vascular Biology Program, Children's Hospital Boston, Department of Surgery, Harvard Medical School, Boston, Massachusetts, USA
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