1
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Yang X, Xia Y, Wang S, Sun C. Prognostic value of SPARC in hepatocellular carcinoma: A systematic review and meta-analysis. PLoS One 2022; 17:e0273317. [PMID: 35981080 PMCID: PMC9387809 DOI: 10.1371/journal.pone.0273317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 08/06/2022] [Indexed: 01/30/2023] Open
Abstract
Objective
Hepatocellular carcinoma (HCC) is characterized by a high degree of malignancy, rapid proliferation of tumor cells, and early liver metastasis. Resistance to multiple drugs independent of the high expression of secreted protein acidic and rich in cysteine (SPARC) is associated with a high risk of recurrence and mortality. However, the prognostic value of SPARC in patients with HCC remains unclear. Therefore, we performed a meta-analysis to evaluate the relationship between the expression of SPARC and the prognosis of patients with HCC.
Methods
We searched for relevant articles in the CNKI, PubMed, EMBASE, and Web of Science databases. The 95% confidence intervals (CIs) were calculated for combined overall survival (OS) and disease-free survival (DFS) to assess the prognostic value of expression of SPARC in patients with HCC.
Results
In six of the studies, SPARC expression status was significantly associated with OS (combined hazard ratio [HR], 1.38; 95% CI, 1.0–1.82; Z = 2.27, P = 0.02) but not with DFS (combined HR, 0.79; 95% CI, 0.16–4.00, Z = 0.28, P = 0.78). Therefore, it cannot be assumed that upregulated SPARC expression has an effect on DFS in patients with HCC.
Conclusion
Elevated SPARC expression is associated with a low survival rate but not with DFS in patients with HCC. Further studies are needed to confirm our conclusions.
Registration
INPLASY registration number: INPLASY202180115. https://inplasy.com/inplasy-2021-8-0115/.
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Affiliation(s)
- Xiaoyu Yang
- Department of Oncology, The Fourth Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
| | - Yunhong Xia
- Department of Oncology, The Fourth Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- * E-mail:
| | - Shuomin Wang
- Department of Oncology, The Fourth Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
| | - Chen Sun
- Department of Oncology, The Fourth Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
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2
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Hypermethylation-Mediated Silencing of CIDEA, MAL and PCDH17 Tumour Suppressor Genes in Canine DLBCL: From Multi-Omics Analyses to Mechanistic Studies. Int J Mol Sci 2022; 23:ijms23074021. [PMID: 35409379 PMCID: PMC9000013 DOI: 10.3390/ijms23074021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 03/30/2022] [Accepted: 04/01/2022] [Indexed: 11/23/2022] Open
Abstract
Gene expression is controlled by epigenetic deregulation, a hallmark of cancer. The DNA methylome of canine diffuse large B-cell lymphoma (cDLBCL), the most frequent malignancy of B-lymphocytes in dog, has recently been investigated, suggesting that aberrant hypermethylation of CpG loci is associated with gene silencing. Here, we used a multi-omics approach (DNA methylome, transcriptome and copy number variations) combined with functional in vitro assays, to identify putative tumour suppressor genes subjected to DNA methylation in cDLBCL. Using four cDLBCL primary cell cultures and CLBL-1 cells, we found that CiDEA, MAL and PCDH17, which were significantly suppressed in DLBCL samples, were hypermethylated and also responsive (at the DNA, mRNA and protein level) to pharmacological unmasking with hypomethylating drugs and histone deacetylase inhibitors. The regulatory mechanism underneath the methylation-dependent inhibition of those target genes expression was then investigated through luciferase and in vitro methylation assays. In the most responsive CpG-rich regions, an in silico analysis allowed the prediction of putative transcription factor binding sites influenced by DNA methylation. Interestingly, regulatory elements for AP2, MZF1, NF-kB, PAX5 and SP1 were commonly identified in all three genes. This study provides a foundation for characterisation and experimental validation of novel epigenetically-dysregulated pathways in cDLBCL.
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3
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Wada K, Misaka T, Yokokawa T, Kimishima Y, Kaneshiro T, Oikawa M, Yoshihisa A, Takeishi Y. Blood-Based Epigenetic Markers of FKBP5 Gene Methylation in Patients With Dilated Cardiomyopathy. J Am Heart Assoc 2021; 10:e021101. [PMID: 34713710 PMCID: PMC8751844 DOI: 10.1161/jaha.121.021101] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Background Blood‐based DNA methylation patterns are linked to types of diseases. FKBP prolyl isomerase 5 (FKBP5), a protein cochaperone, is known to be associated with the inflammatory response, but the regulatory mechanisms by leukocyte FKBP5 DNA methylation in patients with dilated cardiomyopathy (DCM) remain unclear. Methods and Results The present study enrolled patients with DCM (n=31) and age‐matched and sex‐matched control participants (n=43). We assessed FKBP5 CpG (cytosine‐phosphate‐guanine) methylation of CpG islands at the 5′ side as well as putative promoter regions by methylation‐specific quantitative polymerase chain reaction using leukocyte DNA isolated from the peripheral blood. FKBP5 CpG methylation levels at the CpG island of the gene body and the promoter regions were significantly decreased in patients with DCM. Leukocyte FKBP5 and IL‐1β (interleukin 1β) mRNA expression levels were significantly higher in patients with DCM than in controls. The protein expressions of DNMT1 (DNA methyltransferase 1) and DNMT3A (DNA methyltransferase 3A) in leukocytes were significantly reduced in patients with DCM. In vitro methylation assay revealed that FKBP5 promoter activity was inhibited at the methylated conditions in response to immune stimulation, suggesting that the decreased FKBP5 CpG methylation was functionally associated with elevation of FKBP5 mRNA expressions. Histological analysis using a mouse model with pressure overload showed that FKBP5‐expressing cells were substantially infiltrated in the myocardial interstitium in the failing hearts, indicating a possible role of FKBP5 expressions of immune cells in the cardiac remodeling. Conclusions Our findings demonstrate a link between specific CpG hypomethylation of leukocyte FKBP5 and DCM. Blood‐based epigenetic modification in FKBP5 may be a novel molecular mechanism that contributes to the pathogenesis of DCM.
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Affiliation(s)
- Kento Wada
- Department of Cardiovascular Medicine Fukushima Medical University Fukushima Japan
| | - Tomofumi Misaka
- Department of Cardiovascular Medicine Fukushima Medical University Fukushima Japan
| | - Tetsuro Yokokawa
- Department of Cardiovascular Medicine Fukushima Medical University Fukushima Japan
| | - Yusuke Kimishima
- Department of Cardiovascular Medicine Fukushima Medical University Fukushima Japan
| | - Takashi Kaneshiro
- Department of Cardiovascular Medicine Fukushima Medical University Fukushima Japan.,Department of Arrhythmia and Cardiac Pacing Fukushima Medical University Fukushima Japan
| | - Masayoshi Oikawa
- Department of Cardiovascular Medicine Fukushima Medical University Fukushima Japan
| | - Akiomi Yoshihisa
- Department of Cardiovascular Medicine Fukushima Medical University Fukushima Japan.,Department of Clinical Laboratory Sciences Fukushima Medical University School of Health Science Fukushima Japan
| | - Yasuchika Takeishi
- Department of Cardiovascular Medicine Fukushima Medical University Fukushima Japan
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4
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Gao YP, Li L, Yan J, Hou XX, Jia YX, Chang ZW, Guan XY, Qin YR. Down-Regulation of CIDEA Promoted Tumor Growth and Contributed to Cisplatin Resistance by Regulating the JNK-p21/Bad Signaling Pathways in Esophageal Squamous Cell Carcinoma. Front Oncol 2021; 10:627845. [PMID: 33614508 PMCID: PMC7888273 DOI: 10.3389/fonc.2020.627845] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 12/15/2020] [Indexed: 12/24/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most common malignancies with poor prognosis and lack of effective targeted therapies. In this study, we investigated the tumor suppressive role of the cell death inducing DFF like effector A (CIDEA) in ESCC. Firstly, public datasets and ESCC tissue microarray analysis showed that CIDEA was frequently down-regulated at both the mRNA and protein level. This was significantly associated with low differentiation and TNM stage in ESCC, and indicated poor prognosis for ESCC patients. Bisulfite genomic sequencing (BGS) and methylation-specific PCR (MSP) analysis revealed that the down-regulation of CIDEA was associated with hypermethylation of its promoter, which was also correlated with the poor prognosis in ESCC patients. In vitro and in vivo functional studies demonstrated that CIDEA decreased cell growth, foci formation, DNA replication, and tumorigenesis in nude mice. Further study revealed that, during starvation or cisplatin induced DNA damage, CIDEA facilitated the G1-phase arrest or caspase-dependent mitochondrial apoptosis through the JNK-p21/Bad pathway. Therefore, CIDEA is a novel tumor suppressor gene that plays an important role in the development and progression of ESCC, and may provide a potential therapeutic target for patients with ESCC.
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Affiliation(s)
- Ya-Ping Gao
- Department of Clinical Oncology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Lei Li
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong, China
| | - Jie Yan
- Department of Clinical Oncology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Xiao-Xia Hou
- Department of Clinical Oncology, The Third Peoples Hospital of Zhengzhou, Zhengzhou, China
| | - Yong-Xu Jia
- Department of Clinical Oncology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Zhi-Wei Chang
- Department of Clinical Oncology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Xin-Yuan Guan
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong, China
| | - Yan-Ru Qin
- Department of Clinical Oncology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
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5
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Chen J, Zhang J, Gao Y, Li Y, Feng C, Song C, Ning Z, Zhou X, Zhao J, Feng M, Zhang Y, Wei L, Pan Q, Jiang Y, Qian F, Han J, Yang Y, Wang Q, Li C. LncSEA: a platform for long non-coding RNA related sets and enrichment analysis. Nucleic Acids Res 2021; 49:D969-D980. [PMID: 33045741 PMCID: PMC7778898 DOI: 10.1093/nar/gkaa806] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/03/2020] [Accepted: 09/30/2020] [Indexed: 02/01/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been proven to play important roles in transcriptional processes and various biological functions. Establishing a comprehensive collection of human lncRNA sets is urgent work at present. Using reference lncRNA sets, enrichment analyses will be useful for analyzing lncRNA lists of interest submitted by users. Therefore, we developed a human lncRNA sets database, called LncSEA, which aimed to document a large number of available resources for human lncRNA sets and provide annotation and enrichment analyses for lncRNAs. LncSEA supports >40 000 lncRNA reference sets across 18 categories and 66 sub-categories, and covers over 50 000 lncRNAs. We not only collected lncRNA sets based on downstream regulatory data sources, but also identified a large number of lncRNA sets regulated by upstream transcription factors (TFs) and DNA regulatory elements by integrating TF ChIP-seq, DNase-seq, ATAC-seq and H3K27ac ChIP-seq data. Importantly, LncSEA provides annotation and enrichment analyses of lncRNA sets associated with upstream regulators and downstream targets. In summary, LncSEA is a powerful platform that provides a variety of types of lncRNA sets for users, and supports lncRNA annotations and enrichment analyses. The LncSEA database is freely accessible at http://bio.liclab.net/LncSEA/index.php.
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Affiliation(s)
- Jiaxin Chen
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Jian Zhang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Yu Gao
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Yanyu Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Chenchen Feng
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Chao Song
- Department of Pharmacology, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Ziyu Ning
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Xinyuan Zhou
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Jianmei Zhao
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Minghong Feng
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Yuexin Zhang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Ling Wei
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Qi Pan
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Yong Jiang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Fengcui Qian
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Junwei Han
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yongsan Yang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Qiuyu Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Chunquan Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
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6
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Liao LE, Hu DD, Zheng Y. A Four-Methylated lncRNAs-Based Prognostic Signature for Hepatocellular Carcinoma. Genes (Basel) 2020; 11:genes11080908. [PMID: 32784402 PMCID: PMC7463540 DOI: 10.3390/genes11080908] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/21/2020] [Accepted: 08/06/2020] [Indexed: 02/01/2023] Open
Abstract
Currently, an increasing number of studies suggest that long non-coding RNAs (lncRNAs) and methylation-regulated lncRNAs play a critical role in the pathogenesis of various cancers including hepatocellular carcinoma (HCC). Therefore, methylated differentially expressed lncRNAs (MDELs) may be critical biomarkers of HCC. In this study, 63 MDELs were identified by screening The Cancer Genome Atlas (TCGA) HCC lncRNAs expression data set and lncRNAs methylation data set. Based on univariate and multivariate survival analysis, four MDELs (AC025016.1, LINC01164, LINC01183 and LINC01269) were selected to construct the survival prognosis prediction model. Through the PI formula, the study indicates that our new prediction model performed well and is superior to the traditional staging method. At the same time, compared with the previous prediction models reported in the literature, the results of time-dependent receiver operating characteristic (ROC) curve analysis show that our 4-MDELs model predicted overall survival (OS) stability and provided better prognosis. In addition, we also applied the prognostic model to Cancer Cell Line Encyclopedia (CCLE) cell lines and classified different hepatoma cell lines through the model to evaluate the sensitivity of different hepatoma cell lines to different drugs. In conclusion, we have established a new risk scoring system to predict the prognosis, which may have a very important guiding significance for the individualized treatment of HCC patients.
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Affiliation(s)
- Le-En Liao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, Guangdong, China; (L.-E.L.); (D.-D.H.)
- Department of Colorectal Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, Guangdong, China
| | - Dan-Dan Hu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, Guangdong, China; (L.-E.L.); (D.-D.H.)
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, Guangdong, China
| | - Yun Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, Guangdong, China; (L.-E.L.); (D.-D.H.)
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, Guangdong, China
- Correspondence: ; Tel.: +86-20-8734-3676
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7
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Li Y, Zhang XM, Luan MW, Xing JF, Chen J, Xie SQ. Distribution Patterns of DNA N6-Methyladenosine Modification in Non-coding RNA Genes. Front Genet 2020; 11:268. [PMID: 32265991 PMCID: PMC7105833 DOI: 10.3389/fgene.2020.00268] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/05/2020] [Indexed: 01/20/2023] Open
Abstract
N6-methyladenosine (6mA) DNA modification played an important role in epigenetic regulation of gene expression. And the aberrational expression of non-coding genes, as important regular elements of gene expression, was related to many diseases. However, the distribution and potential functions of 6mA modification in non-coding RNA (ncRNA) genes are still unknown. In this study, we analyzed the 6mA distribution of ncRNA genes and compared them with protein-coding genes in four species (Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, and Homo sapiens) using single-molecule real-time (SMRT) sequencing data. The results indicated that the consensus motifs of short nucleotides at 6mA location were highly conserved in four species, and the non-coding gene was less likely to be methylated compared with protein-coding gene. Especially, the 6mA-methylated lncRNA genes were expressed significant lower than genes without methylation in A. thaliana (p = 3.295e-4), D. melanogaster (p = 3.439e-11), and H. sapiens (p = 9.087e-3). The detection and distribution profiling of 6mA modification in ncRNA regions from four species reveal that 6mA modifications may have effects on their expression level.
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Affiliation(s)
- Yu Li
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Hainan University, Haikou, China
| | - Xiao-Ming Zhang
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Huhhot, China
| | - Mei-Wei Luan
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Hainan University, Haikou, China
| | - Jian-Feng Xing
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Hainan University, Haikou, China
| | - Jianguo Chen
- School of Life Sciences, Hubei University, Wuhan, China
| | - Shang-Qian Xie
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Hainan University, Haikou, China
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8
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Zhi H, Li X, Wang P, Gao Y, Gao B, Zhou D, Zhang Y, Guo M, Yue M, Shen W, Ning S, Jin L, Li X. Lnc2Meth: a manually curated database of regulatory relationships between long non-coding RNAs and DNA methylation associated with human disease. Nucleic Acids Res 2019; 46:D133-D138. [PMID: 29069510 PMCID: PMC5753220 DOI: 10.1093/nar/gkx985] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 10/13/2017] [Indexed: 02/01/2023] Open
Abstract
Lnc2Meth (http://www.bio-bigdata.com/Lnc2Meth/), an interactive resource to identify regulatory relationships between human long non-coding RNAs (lncRNAs) and DNA methylation, is not only a manually curated collection and annotation of experimentally supported lncRNAs-DNA methylation associations but also a platform that effectively integrates tools for calculating and identifying the differentially methylated lncRNAs and protein-coding genes (PCGs) in diverse human diseases. The resource provides: (i) advanced search possibilities, e.g. retrieval of the database by searching the lncRNA symbol of interest, DNA methylation patterns, regulatory mechanisms and disease types; (ii) abundant computationally calculated DNA methylation array profiles for the lncRNAs and PCGs; (iii) the prognostic values for each hit transcript calculated from the patients clinical data; (iv) a genome browser to display the DNA methylation landscape of the lncRNA transcripts for a specific type of disease; (v) tools to re-annotate probes to lncRNA loci and identify the differential methylation patterns for lncRNAs and PCGs with user-supplied external datasets; (vi) an R package (LncDM) to complete the differentially methylated lncRNAs identification and visualization with local computers. Lnc2Meth provides a timely and valuable resource that can be applied to significantly expand our understanding of the regulatory relationships between lncRNAs and DNA methylation in various human diseases.
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Affiliation(s)
- Hui Zhi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xin Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Peng Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yue Gao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Baoqing Gao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Dianshuang Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Maoni Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Ming Yue
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Weitao Shen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Lianhong Jin
- Affiliation Department of Histology and Embryology, Harbin Medical University, Harbin 150081, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
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9
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Hu XQ, Chen M, Dasgupta C, Xiao D, Huang X, Yang S, Zhang L. Chronic hypoxia upregulates DNA methyltransferase and represses large conductance Ca2+-activated K+ channel function in ovine uterine arteries. Biol Reprod 2018; 96:424-434. [PMID: 28203702 DOI: 10.1095/biolreprod.116.145946] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/23/2016] [Accepted: 12/19/2016] [Indexed: 01/06/2023] Open
Abstract
Chronic hypoxia during gestation suppresses large-conductance Ca2+-activated K+ (BKCa) channel function and impedes uterine arterial adaptation to pregnancy. This study tested the hypothesis that chronic hypoxia has a direct effect in upregulating DNA methyltransferase (DNMT) and epigenetically repressing BKCa channel beta-1 subunit (KCNMB1) expression in uterine arteries. Resistance-sized uterine arteries were isolated from near-term pregnant sheep maintained at ∼300 m above sea level or animals acclimatized to high-altitude (3,801 m) hypoxia for 110 days during gestation. For ex vivo hypoxia treatment, uterine arteries from normoxic animals were treated with 21.0% O2 or 10.5% O2 for 48 h. High-altitude hypoxia significantly upregulated DNMT3b expression and enzyme activity in uterine arteries. Similarly, ex vivo hypoxia treatment upregulated DNMT3b expression and enzyme activity that was blocked by a DNMT inhibitor 5-aza-2'-deoxycytidine (5-Aza). Of importance, 5-Aza inhibited hypoxia-induced hypermethylation of specificity protein (SP) 1 binding site at the KCNMB1 promoter and restored transcription factor binding to the KCNMB1 promoter, resulting in the recovery of KCNMB1 gene expression in uterine arteries. Furthermore, 5-Aza blocked the effect of hypoxia and rescued BKCa channel activity and reversed hypoxia-induced decrease in BKCa channel-mediated relaxations and increase in myogenic tone of uterine arteries. Collectively, these results suggest that chronic hypoxia during gestation upregulates DNMT expression and activity, resulting in hypermethylation and repression of KCNMB1 gene and BKCa channel function, impeding uterine arterial adaptation to pregnancy.
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Affiliation(s)
- Xiang-Qun Hu
- Center for Perinatal Biology, Division of Pharmacology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California, USA
| | - Man Chen
- Center for Perinatal Biology, Division of Pharmacology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California, USA
| | - Chiranjib Dasgupta
- Center for Perinatal Biology, Division of Pharmacology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California, USA
| | - Daliao Xiao
- Center for Perinatal Biology, Division of Pharmacology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California, USA
| | - Xiaohui Huang
- Center for Perinatal Biology, Division of Pharmacology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California, USA
| | - Shumei Yang
- Department of Chemistry and Biochemistry, California State University, San Bernardino, California, USA
| | - Lubo Zhang
- Center for Perinatal Biology, Division of Pharmacology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California, USA
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10
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Liu X, Zhou P, Fan F, Li D, Wu J, Lu Y, Luo Y. CpG site methylation in CRYAA promoter affect transcription factor Sp1 binding in human lens epithelial cells. BMC Ophthalmol 2016; 16:141. [PMID: 27507241 PMCID: PMC4979130 DOI: 10.1186/s12886-016-0309-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 07/28/2016] [Indexed: 10/26/2022] Open
Abstract
BACKGROUND Age-related cataract (ARC) is the leading cause of visual impairment worldwide, and α-crystallin (CRYAA) is the predominant structural protein involved in the maintenance of lens clarity and refractive properties. We previously demonstrated that CRYAA genes undergo epigenetic repression in the lens epithelia in ARC. We further analyze the underlying mechanism in the current study. METHODS The transcription factor binding sites of the CpG island of CRYAA promoter were predicted by TESS website. An electrophoretic mobility shift assay (EMSA) was used to analyze the impact of the methylation of CpG sites on transcription factors. Human lens epithelial B-3 (HLE B-3) Cells were treated with demethylation agent zebularine in the concentrations of 0 (PBS as control), 10 μM, 20 μM, 50 μM, 100 μM and 200 μM, respectively. After treatment in the above concentrations for 24 h, 48 h and 72 h, respectively, CRYAA mRNA expression levels were detected by Quantitative Real-Time RT-PCR. RESULTS The methylation of the CpG site of the CRYAA promoter decreased the DNA-binding capacity of transcription factor Sp1. Zebularine increased CRYAA expression in HLE B-3 Cells in a dose- dependent and time- dependent pattern. CONCLUSIONS The evidence presented suggests that the methylation of the CpG sites of the CRYAA promotor directly affect Sp1 binding, leading to down expression of CRYAA in human lens epithelial cells. Zebularine treatment could restore CRYAA expression in a dose- dependent and time- dependent pattern.
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Affiliation(s)
- Xin Liu
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, 83 FenYang Road, Shanghai, 200031, People's Republic of China.,Key Laboratory of Myopia, Ministry of Health, 83 FenYang Road, Shanghai, 200031, People's Republic of China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, 83 FenYang Road, Shanghai, 200031, People's Republic of China
| | - Peng Zhou
- Department of Ophthalmology, Parkway Health, Specialty and Inpatient Center (Luwan), 170 DanShui Road, Floor 3, Shanghai, 200020, People's Republic of China.,Hong Qiao Medical Center, 2258 HongQiao Road, Shanghai, 200033, People's Republic of China
| | - Fan Fan
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, 83 FenYang Road, Shanghai, 200031, People's Republic of China.,Key Laboratory of Myopia, Ministry of Health, 83 FenYang Road, Shanghai, 200031, People's Republic of China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, 83 FenYang Road, Shanghai, 200031, People's Republic of China
| | - Dan Li
- Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, 83 FenYang Road, Shanghai, 200031, People's Republic of China
| | - Jihong Wu
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, 83 FenYang Road, Shanghai, 200031, People's Republic of China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, 83 FenYang Road, Shanghai, 200031, People's Republic of China
| | - Yi Lu
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, 83 FenYang Road, Shanghai, 200031, People's Republic of China.,Key Laboratory of Myopia, Ministry of Health, 83 FenYang Road, Shanghai, 200031, People's Republic of China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, 83 FenYang Road, Shanghai, 200031, People's Republic of China
| | - Yi Luo
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, 83 FenYang Road, Shanghai, 200031, People's Republic of China. .,Key Laboratory of Myopia, Ministry of Health, 83 FenYang Road, Shanghai, 200031, People's Republic of China. .,Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, 83 FenYang Road, Shanghai, 200031, People's Republic of China.
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11
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PPARγ regulated CIDEA affects pro-apoptotic responses in glioblastoma. Cell Death Discov 2015; 1:15038. [PMID: 27551468 PMCID: PMC4979534 DOI: 10.1038/cddiscovery.2015.38] [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: 08/13/2015] [Accepted: 08/19/2015] [Indexed: 02/07/2023] Open
Abstract
Refractoriness of glioblastoma multiforme (GBM) to current treatment paradigms has necessitated identification of new targets to better the existing therapeutic strategies. One such target is peroxisome proliferator-activated receptor gamma (PPARγ) - a transcription factor involved in regulation of lipid metabolism and inflammation. Expression of PPARγ, a known regulator of cell death-inducing DFFA-like effector (CIDEA), is modulated by hypoxia inducible factor (HIF-1α). While the involvement of CIDEA in lipid metabolism is known, its role in malignancies remains largely unknown. An elevated PPARγ and low CIDEA level was observed in GBM tumors as compared with surrounding non-neoplastic tissue. As reciprocal relation exists between PPAR and HIF-1α: and as HIF-1α is a key component in glioma progression, their role in regulating CIDEA expression in glioblastoma was investigated. Although HIF-1α inhibition had no effect on CIDEA expression, pharmacological inhibition of PPARγ elevated CIDEA levels. PPARγ mediated upregulation of CIDEA was accompanied by decreased recruitment of NFκB and SP1 to their predicted binding sites on CIDEA promoter. Ectopic expression of CIDEA triggered apoptosis, activated JNK, decreased HIF-1α activation and increased PPARγ levels in glioma cells. While CIDEA overexpression induced actin cytoskeletal disruption, cell cycle arrest, release of pro-inflammatory cytokine IL-6 in a JNK-dependent manner; CIDEA mediated apoptotic cell death, decreased STAT3 phosphorylation and increased p53 acetylation was JNK independent. This study highlights for the first time the existence of (i) PPARγ-CIDEA regulatory loop in glioma and (ii) novel function of CIDEA as regulator of glioma cell survival.
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Kong Q, Hai T, Ma J, Huang T, Jiang D, Xie B, Wu M, Wang J, Song Y, Wang Y, He Y, Sun J, Hu K, Guo R, Wang L, Zhou Q, Mu Y, Liu Z. Rosa26 locus supports tissue-specific promoter driving transgene expression specifically in pig. PLoS One 2014; 9:e107945. [PMID: 25232950 PMCID: PMC4169413 DOI: 10.1371/journal.pone.0107945] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 08/17/2014] [Indexed: 11/19/2022] Open
Abstract
Genetically modified pigs have become a popular model system in fundamental research, agricultural and biomedical applications. However, random integration often result in unstable expression of transgene and unpredictable phenotypes. The Rosa26 locus has been widely used to produce genetic modified animals with high and consistent expressing of transgene in mouse, human and rat, as it can be targeted efficiently and is not subject to gene-silencing effects. Recently, the first case of reporter gene targeting pigs in porcine Rosa26 (pRosa26) locus was reported. In the study, full sequence of pRosa26 locus was further characterized, and the pRosa26 promoter (pR26) was cloned and we evidenced that the new porcine endogenous promoter is suitable for driving transgene expression in a high and stable manner by avoiding DNA methylation. Furthermore, elongation factor 1a promoter (EF1a) -driven GFP reporter and Myostatin promoter (MyoP)-driven Follistatin (Fst) were successfully targeted into the pRosa26 locusby traditional homologous recombination (HR) strategy. EF1a showed high activity and hypomethylation at the locus. And, muscle-specific promoter MyoP was activated strictly in muscle of the pRosa26 targeted pigs, indicating Rosa26 locus supports tissue-specific promoter driving transgene expression in its own manner. The study provided further demonstration on biomedical and agricultural applications of porcine Rosa26 promoter and locus.
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Affiliation(s)
- Qingran Kong
- Laboratory of Embryo Biotechnology, College of life science, Northeast Agricultural University, Harbin, China
| | - Tang Hai
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jing Ma
- Laboratory of Embryo Biotechnology, College of life science, Northeast Agricultural University, Harbin, China
| | - Tianqing Huang
- Laboratory of Embryo Biotechnology, College of life science, Northeast Agricultural University, Harbin, China
| | - Dandan Jiang
- Laboratory of Embryo Biotechnology, College of life science, Northeast Agricultural University, Harbin, China
| | - Bingteng Xie
- Laboratory of Embryo Biotechnology, College of life science, Northeast Agricultural University, Harbin, China
| | - Meiling Wu
- Laboratory of Embryo Biotechnology, College of life science, Northeast Agricultural University, Harbin, China
| | - Jiaqiang Wang
- Laboratory of Embryo Biotechnology, College of life science, Northeast Agricultural University, Harbin, China
| | - Yuran Song
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Graduate University of the Chinese Academy of Sciences, Beijing, China
| | - Ying Wang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yilong He
- Laboratory of Embryo Biotechnology, College of life science, Northeast Agricultural University, Harbin, China
| | - Jialu Sun
- Laboratory of Embryo Biotechnology, College of life science, Northeast Agricultural University, Harbin, China
| | - Kui Hu
- Laboratory of Embryo Biotechnology, College of life science, Northeast Agricultural University, Harbin, China
| | - Runfa Guo
- Laboratory of Embryo Biotechnology, College of life science, Northeast Agricultural University, Harbin, China
| | - Liu Wang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qi Zhou
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yanshuang Mu
- Laboratory of Embryo Biotechnology, College of life science, Northeast Agricultural University, Harbin, China
| | - Zhonghua Liu
- Laboratory of Embryo Biotechnology, College of life science, Northeast Agricultural University, Harbin, China
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13
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Chung Y, Fu E. Cyclosporine A up-regulates Sonic hedgehog in gingiva: role of the up-regulation on gingival cell proliferation. J Periodontal Res 2014; 49:810-6. [PMID: 24823913 DOI: 10.1111/jre.12168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2013] [Indexed: 11/28/2022]
Abstract
BACKGROUND AND OBJECTIVE Sonic hedgehog protein (SHH) is a mitogen that stimulates cell proliferation. Cyclosporine A enhances the proliferation of gingival cells; however, the relationships of SHH to cyclosporine A or to cyclosporine A-enhanced gingival cell proliferation have not been described. MATERIAL AND METHODS Here, we investigated SHH expression in gingiva in vitro and in vivo after cyclosporine A treatment and tested the effect of SHH inhibition on cyclosporine A-enhanced gingival fibroblast proliferation in vitro. RESULTS In human gingival fibroblasts, cyclosporine A treatment increased the expression of SHH transcripts and SHH protein, and stimulated cell proliferation; the addition of cyclopamine, an SHH signaling inhibitor, suppressed cyclosporine A-enhanced cell proliferation. Up-regulated expression of SHH and up-regulation of proliferating cell nuclear antigen transcripts and protein were observed in the edentulous gingiva of cyclosporine A-treated rats. CONCLUSION Cyclosporine A up-regulates gingival SHH expression in vitro and in vivo, and the inhibition of the SHH pathway counteracts the stimulatory effect of cyclosporine A on gingival fibroblast proliferation. Therefore, we suggest that SHH mediates a novel molecular mechanism for cyclosporine A-induced gingival complications.
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Affiliation(s)
- Y Chung
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, China; Department of Periodontology, School of Dentistry, National Defense Medical Center and Tri-Service General Hospital, Taipei, Taiwan, China
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Ibragimova I, Dulaimi E, Slifker MJ, Chen DY, Uzzo RG, Cairns P. A global profile of gene promoter methylation in treatment-naïve urothelial cancer. Epigenetics 2014; 9:760-73. [PMID: 24521710 PMCID: PMC4063835 DOI: 10.4161/epi.28078] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The epigenetic alteration of aberrant hypermethylation in the promoter CpG island of a gene is associated with repression of transcription. In neoplastic cells, aberrant hypermethylation is well described as a mechanism of allele inactivation of particular genes with a tumor suppressor function. To investigate the role of aberrant hypermethylation in the biology and progression of urothelial cancer, we examined 101 urothelial (transitional cell) carcinomas (UC), broadly representative of the disease at presentation, with no prior immunotherapy, chemotherapy or radiotherapy, by Infinium HM27 containing 14,495 genes. The genome-wide signature of aberrant promoter hypermethylation in UC consisted of 729 genes significant by a Wilcoxon test, hypermethylated in a CpG island within 1 kb of the transcriptional start site and unmethylated in normal urothelium from aged individuals. We examined differences in gene methylation between the two main groups of UC: the 75% that are superficial, which often recur but rarely progress, and the 25% with muscle invasion and poor prognosis. We further examined pairwise comparisons of the pathologic subgroups of high or low grade, invasive or non-invasive (pTa), and high grade superficial or low grade superficial UC. Pathways analysis indicated over-representation of genes involved in cell adhesion or metabolism in muscle-invasive UC. Notably, the TET2 epigenetic regulator was one of only two genes more frequently methylated in superficial tumors and the sole gene in low grade UC. Other chromatin remodeling genes, MLL3 and ACTL6B, also showed aberrant hypermethylation. The Infinium methylation value for representative genes was verified by pyrosequencing. An available mRNA expression data set indicated many of the hypermethylated genes of interest to be downregulated in UC. Unsupervised clustering of the most differentially methylated genes distinguished muscle invasive from superficial UC. After filtering, cluster analysis showed a CpG Island Methylator Phenotype (CIMP)-like pattern of widespread methylation in 11 (11%) tumors. Nine of these 11 tumors had hypermethylation of TET2. Our analysis provides a basis for further studies of hypermethylation in the development and progression of UC.
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Affiliation(s)
- Ilsiya Ibragimova
- Cancer Epigenetics Program; Fox Chase Cancer Center; Philadelphia PA, USA
| | - Essel Dulaimi
- Department of Pathology; Fox Chase Cancer Center; Philadelphia PA, USA
| | - Michael J Slifker
- Department of Biostatistics and Bioinformatics; Fox Chase Cancer Center; Philadelphia PA, USA
| | - David Y Chen
- Department of Urology; Fox Chase Cancer Center; Philadelphia PA, USA
| | - Robert G Uzzo
- Department of Urology; Fox Chase Cancer Center; Philadelphia PA, USA
| | - Paul Cairns
- Cancer Epigenetics Program; Fox Chase Cancer Center; Philadelphia PA, USA
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Carr SK, Chen JH, Cooper WN, Constância M, Yeo GSH, Ozanne SE. Maternal diet amplifies the hepatic aging trajectory of Cidea in male mice and leads to the development of fatty liver. FASEB J 2014; 28:2191-201. [PMID: 24481968 DOI: 10.1096/fj.13-242727] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The importance of the early environment on long-term heath and life span is well documented. However, the molecular mechanisms mediating these effects remain poorly understood. Male offspring from a maternal protein restriction model, in which animals are exposed to a low-protein diet while in utero and then are cross-fostered to normally fed dams, demonstrate low birth weight, catch-up growth, and reduced life span (recuperated offspring). In the current study, we used microarray analysis to identify hepatic genes that changed with age. Cell death-inducing DNA fragmentation factor, α subunit-like effector A (Cidea), a transcriptional coactivator that has been implicated in lipid accumulation demonstrated one of the largest age-associated increases in expression (200-fold, P<0.001). This increase was exaggerated ∼3-fold in recuperated offspring. These demonstrated increased hepatic lipid accumulation, higher levels of transcription factors important in lipid regulation, and greater oxidative stress. In vitro analysis revealed that Cidea expression was regulated by oxidative stress and DNA methylation. These findings suggest that maternal diet modulates the age-associated changes in Cidea expression through several mechanisms. This expression affects hepatic lipid metabolism in these animals and thus provides a mechanism by which maternal diet can contribute to the metabolic health and ultimately the life span of the offspring.
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Affiliation(s)
- Sarah K Carr
- 1University of Cambridge Metabolic Research Laboratories, MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, Level 4, Box 289, Addenbrooke's Hospital, Cambridge CB2 OQQ, UK.
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16
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Elhaik E, Pellegrini M, Tatarinova TV. Gene expression and nucleotide composition are associated with genic methylation level in Oryza sativa. BMC Bioinformatics 2014; 15:23. [PMID: 24447369 PMCID: PMC3903047 DOI: 10.1186/1471-2105-15-23] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 12/26/2013] [Indexed: 12/21/2022] Open
Abstract
Background The methylation of cytosines at CpG dinucleotides, which plays an important role in gene expression regulation, is one of the most studied epigenetic modifications. Thus far, the detection of DNA methylation has been determined mostly by experimental methods, which are not only prone to bench effects and artifacts but are also time-consuming, expensive, and cannot be easily scaled up to many samples. It is therefore useful to develop computational prediction methods for DNA methylation. Our previous studies highlighted the existence of correlations between the GC content of the third codon position (GC3), methylation, and gene expression. We thus designed a model to predict methylation in Oryza sativa based on genomic sequence features and gene expression data. Results We first derive equations to describe the relationship between gene methylation levels, GC3, expression, length, and other gene compositional features. We next assess gene compositional features involving sixmers and their association with methylation levels and other gene level properties. By applying our sixmer-based approach on rice gene expression data we show that it can accurately predict methylation (Pearson’s correlation coefficient r = 0.79) for the majority (79%) of the genes. Matlab code with our model is included. Conclusions Gene expression variation can be used as predictors of gene methylation levels.
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Affiliation(s)
| | | | - Tatiana V Tatarinova
- Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, 4650 Sunset Blvd, Los Angeles, CA 90027, USA.
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17
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Core promoter analysis of porcine Six1 gene and its regulation of the promoter activity by CpG methylation. Gene 2013; 529:238-44. [DOI: 10.1016/j.gene.2013.07.102] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Revised: 07/23/2013] [Accepted: 07/27/2013] [Indexed: 11/22/2022]
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18
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Amino acid starvation induces reactivation of silenced transgenes and latent HIV-1 provirus via down-regulation of histone deacetylase 4 (HDAC4). Proc Natl Acad Sci U S A 2012; 109:E2284-93. [PMID: 22826225 DOI: 10.1073/pnas.1202174109] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The epigenetic silencing of exogenous transcriptional units integrated into the genome represents a critical problem both for long-term gene therapy efficacy and for the eradication of latent viral infections. We report here that limitation of essential amino acids, such as methionine and cysteine, causes selective up-regulation of exogenous transgene expression in mammalian cells. Prolonged amino acid deprivation led to significant and reversible increase in the expression levels of stably integrated transgenes transcribed by means of viral or human promoters in HeLa cells. This phenomenon was mediated by epigenetic chromatin modifications, because histone deacetylase (HDAC) inhibitors reproduced starvation-induced transgene up-regulation, and transcriptome analysis, ChIP, and pharmacological and RNAi approaches revealed that a specific class II HDAC, namely HDAC4, plays a critical role in maintaining the silencing of exogenous transgenes. This mechanism was also operational in cells chronically infected with HIV-1, the etiological agent of AIDS, in a latency state. Indeed, both amino acid starvation and pharmacological inhibition of HDAC4 promoted reactivation of HIV-1 transcription and reverse transcriptase activity production in HDAC4(+) ACH-2 T-lymphocytic cells but not in HDAC4(-) U1 promonocytic cells. Thus, amino acid deprivation leads to transcriptional derepression of silenced transgenes, including integrated plasmids and retroviruses, by a process involving inactivation or down-regulation of HDAC4. These findings suggest that selective targeting of HDAC4 might represent a unique strategy for modulating the expression of therapeutic viral vectors, as well as that of integrated HIV-1 proviruses in latent reservoirs without significant cytotoxicity.
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Zhang Y, Yang B, Du Z, Bai T, Gao YT, Wang YJ, Lou C, Wang FM, Bai Y. Aberrant methylation of SPARC in human hepatocellular carcinoma and its clinical implication. World J Gastroenterol 2012; 18:2043-52. [PMID: 22563191 PMCID: PMC3342602 DOI: 10.3748/wjg.v18.i17.2043] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 11/25/2011] [Accepted: 02/27/2012] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the methylation status of secreted protein acidic and rich in cysteine (SPARC) in human hepatocellular carcinoma (HCC) and evaluate its clinical implication.
METHODS: The methylation status of SPARC was analyzed in one HCC cell line (SMMC-7721) and 60 pairs of HCC and corresponding nontumorous tissues by methylation-specific polymerase chain reaction and bisulfite sequencing. The expression of SPARC mRNA and protein were examined by reverse transcription polymerase chain reaction and immunohistochemistry, respectively. The correlations between the methylation status and the gene expression, the clinicopathological parameters, as well as the prognosis after surgery were analyzed.
RESULTS: In the SMMC-7721 cell line, the loss of SPARC expression was correlated with the aberrant methylation and could be reactivated by the demethylating agent 5-aza-2’-deoxycytidine. Methylation frequency of SPARC in HCC was significantly higher than that in the corresponding nontumorous tissues (45/60 vs 7/60, P < 0.001), and it was correlated with the pathological classification (P = 0.019). The downregulation of the SPARC mRNA expression in HCC was correlated with the SPARC methylation (P = 0.040). The patients with methylated SPARC had a poorer overall survival than those without methylated SPARC (28.0 mo vs 41.0 mo, P = 0.043).
CONCLUSION: Aberrant methylation is an important mechanism for SPARC inactivation in HCC and SPARC methylation may be a promising biomarker for the diagnosis and prognosis of HCC.
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Tang X, Xing Z, Tang H, Liang L, Zhao M. Human cell-death-inducing DFF45-like effector C induces apoptosis via caspase-8. Acta Biochim Biophys Sin (Shanghai) 2011; 43:779-86. [PMID: 21865223 DOI: 10.1093/abbs/gmr073] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human cell-death-inducing DNA-fragmentation-factor (DFF45)-like effector C (CIDEC) is a potent apoptotic inducer. Previous studies have indicated that the Fat-specific protein 27 (Fsp27), a mouse homolog of CIDEC, induces apoptosis via caspase-3, -7, and -9 and triggers the release of cytochrome c from mitochondria, which implies that the mitochondrial pathway is involved in Fsp27-induced apoptosis. In the current study, we found that CIDEC-induced apoptosis was mediated by caspase-8. The caspase inhibitor assay showed that CIDEC-induced apoptosis was dramatically reduced in the presence of the general caspase inhibitor, the caspase-3 inhibitor, and the caspase-8 inhibitor, whereas the caspase-9 inhibitor only weakly inhibited CIDEC-induced apoptosis. These results confirmed that the activation of caspase-3 and caspase-8 were involved in CIDEC-induced apoptosis. Moreover, in caspase-3- or caspase-8-deficient cells, CIDEC-induced apoptosis were dramatically decreased, which demonstrated that CIDEC-induced apoptosis might require the activation of caspase-3 and caspase-8. Because caspase-8 in general is a key effecter of death-receptor pathway and activated by Fas-Associated protein with Death Domain (FADD), we examined whether FADD was involved in CIDEC-induced apoptosis. Our results demonstrated that CIDEC-induced apoptosis was independent of FADD, suggesting that CIDEC-induced apoptosis might be in a death-receptor-independent, caspase-8-dependent manner. It was also found that the region of amino acid 168-200 in carboxyl domain of CIDEC was critical for its crucial pro-apoptotic function.
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Affiliation(s)
- Xin Tang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, China
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Singh D, Pannier AK, Zempleni J. Identification of holocarboxylase synthetase chromatin binding sites in human mammary cell lines using the DNA adenine methyltransferase identification technology. Anal Biochem 2011; 413:55-9. [PMID: 21303649 DOI: 10.1016/j.ab.2011.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 01/30/2011] [Accepted: 02/01/2011] [Indexed: 12/28/2022]
Abstract
Holocarboxylase synthetase (HCS) is a chromatin protein that is essential for mediating the covalent binding of biotin to histones. Biotinylation of histones plays crucial roles in the repression of genes and repeats in the human genome. We tested the feasibility of DNA adenine methyltransferase identification (DamID) technology to map HCS binding sites in human mammary cell lines. Full-length HCS was fused to DNA adenine methyltransferase (Dam) for subsequent transfection into breast cancer (MCF-7) and normal breast (MCF-10A) cells. HCS docking sites in chromatin were identified by using the unique adenine methylation sites established by Dam in the fusion construct; docking sites were unambiguously identified using methylation-sensitive digestion, cloning, and sequencing. In total, 15 novel HCS binding sites were identified in the two cell lines, and the following 4 of the 15 overlapped between MCF-7 and MCF-10A cells: inositol polyphosphate-5-phosphatase A, corticotropin hormone precursor, ribosome biogenesis regulatory protein, and leptin precursor. We conclude that DamID is a useful technology to map HCS binding sites in human chromatin and propose that the entire set of HCS binding sites could be mapped by combining DamID with microarray technology.
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Affiliation(s)
- Dipika Singh
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
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22
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Deng GF, Qin JM, Sun XS, Kuang ZY, Su T, Zhao QH, Shi YW, Liu XR, Yu MJ, Yi YH, Liao WP, Long YS. Promoter analysis of mouse Scn3a gene and regulation of the promoter activity by GC box and CpG methylation. J Mol Neurosci 2011; 44:115-21. [PMID: 21271300 DOI: 10.1007/s12031-011-9492-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Accepted: 01/11/2011] [Indexed: 01/04/2023]
Abstract
Voltage-gated sodium channel α-subunit type III (Na(v)1.3) is mainly expressed in the central nervous system and is associated with neurological disorders. The expression of mouse Scn3a product (Na(v)1.3) mainly occurs in embryonic and early postnatal brain but not in adult brain. Here, we report for the first time the identification and characterization of the mouse Scn3a gene promoter region and regulation of the promoter activity by GC box and CpG methylation. Luciferase assay showed that the promoter region F1.2 (nt -1,049 to +157) had significantly higher activity in PC12 cells, comparing with that in SH-SY5Y cells and HEK293 cells. A stepwise 5' truncation of the promoter region found that the minimal functional promoter located within the region nt -168 to +157. Deletion of a GC box (nt -254 to -258) in the mouse Scn3a promoter decreased the promoter activity. CpG methylation of the F1.2 without the GC box completely repressed the promoter activity, suggesting that the GC box is a critical element in the CpG-methylated Scn3a promoter. These results suggest that the GC box and CpG methylation might play important roles in regulating mouse Scn3a gene expression.
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Affiliation(s)
- Guang-Fei Deng
- Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and The Ministry of Education of China, Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University, 250 Chang-gang-dong Road, Guangzhou, China
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Investigation of DNA damage response and apoptotic gene methylation pattern in sporadic breast tumors using high throughput quantitative DNA methylation analysis technology. Mol Cancer 2010; 9:303. [PMID: 21092294 PMCID: PMC3004830 DOI: 10.1186/1476-4598-9-303] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Accepted: 11/23/2010] [Indexed: 01/02/2023] Open
Abstract
Background- Sporadic breast cancer like many other cancers is proposed to be a manifestation of abnormal genetic and epigenetic changes. For the past decade our laboratory has identified genes involved in DNA damage response (DDR), apoptosis and immunesurvelliance pathways to influence sporadic breast cancer risk in north Indian population. Further to enhance our knowledge at the epigenetic level, we performed DNA methylation study involving 17 gene promoter regions belonging to DNA damage response (DDR) and death receptor apoptotic pathway in 162 paired normal and cancerous breast tissues from 81 sporadic breast cancer patients, using a high throughput quantitative DNA methylation analysis technology. Results- The study identified five genes with statistically significant difference between normal and tumor tissues. Hypermethylation of DR5 (P = 0.001), DCR1 (P = 0.00001), DCR2 (P = 0.0000000005) and BRCA2 (P = 0.007) and hypomethylation of DR4 (P = 0.011) in sporadic breast tumor tissues suggested a weak/aberrant activation of the DDR/apoptotic pathway in breast tumorigenesis. Negative correlation was observed between methylation status and transcript expression levels for TRAIL, DR4, CASP8, ATM, CHEK2, BRCA1 and BRCA2 CpG sites. Categorization of the gene methylation with respect to the clinicopathological parameters showed an increase in aberrant methylation pattern in advanced tumors. These uncharacteristic methylation patterns corresponded with decreased death receptor apoptosis (P = 0.047) and DNA damage repair potential (P = 0.004) in advanced tumors. The observation of BRCA2 -26 G/A 5'UTR polymorphism concomitant with the presence of methylation in the promoter region was novel and emerged as a strong candidate for susceptibility to sporadic breast tumors. Conclusion- Our study indicates that methylation of DDR-apoptotic gene promoters in sporadic breast cancer is not a random phenomenon. Progressive epigenetic alterations in advancing tumors result in aberrant DDR-apoptotic pathway thereby promoting tumor development. We propose, since pathological epigenetic changes of the DDR-apoptotic genes are reversible modifications, these could further be targeted for therapeutic interventions.
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Yonezawa T, Kurata R, Kimura M, Inoko H. Which CIDE are you on? Apoptosis and energy metabolism. MOLECULAR BIOSYSTEMS 2010; 7:91-100. [PMID: 20967381 DOI: 10.1039/c0mb00099j] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Around 1998, cell death-inducing DNA fragmentation factor-alpha (DFFA)-like effector (CIDE) proteins including CIDEA, CIDEB and CIDEC/fat specific protein 27 (Fsp27) were first identified by their sequence homology with the N-terminal domain of the DNA fragmentation factor (DFF). Indeed, in vitro analysis revealed that all three CIDE proteins are involved in apoptosis. However, recent gene-targeting studies have provided novel insights into the physiological function of CIDE proteins. Mice deficient in each CIDE protein exhibit lean phenotypes, a reduction of lipid droplet size in white adipose tissue and increased metabolic rate. Thus, all CIDE proteins play an important role in energy metabolism and lipid droplet formation. More recently, a glycoproteomics approach has shown that post-translational regulation of CIDE proteins via glycosylation modulates transforming growth factor (TGF)-beta 1-dependent apoptosis. Another recent study using mouse embryonic fibroblasts derived from CIDEA-deficient mice revealed that 5'AMP-activated protein kinase (AMPK) activity is regulated by CIDEA-mediated ubiquitin-dependent proteasomal degradation via a protein interaction with the AMPK beta subunit. Even after a decade of study, the physiological roles of CIDE proteins have still not been completely elucidated. This review aims to shed light on the novel functions of CIDE proteins and their physiological roles.
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Affiliation(s)
- Tomo Yonezawa
- Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Bohseidai, Ishehara, Kanagawa 259-1193, Japan.
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Min J, Zhang W, Gu Y, Hong L, Yao L, Li F, Zhao D, Feng Y, Zhang H, Li Q. CIDE-3 interacts with lipopolysaccharide-induced tumor necrosis factor, and overexpression increases apoptosis in hepatocellular carcinoma. Med Oncol 2010; 28 Suppl 1:S219-27. [PMID: 20957525 DOI: 10.1007/s12032-010-9702-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Accepted: 09/21/2010] [Indexed: 01/07/2023]
Abstract
Cell death-inducing DFF45-like effector-3 (CIDE-3) is a novel member of an apoptosis-inducing protein family, but its function is unknown. CIDE-3 shows a different distribution pattern in hepatocellular carcinoma (HCC) tissues and normal adjacent tissues. Therefore, this work tested the hypothesis that CIDE-3 induces apoptosis in HCC cells, inhibiting oncogenesis and tumor development. We used immunohistochemistry to evaluate the expression of CIDE-3 in 82 HCC samples and 51 adjacent liver tissues. Overexpression of CIDE-3 induced apoptosis, as detected by flow cytometry, in the HCC cell line SMMC-7721, which had undetectable levels of CIDE-3 in the absence of CIDE-3 overexpression. A yeast two-hybrid system was employed to screen for proteins that interact with CIDE-3. The expression of CIDE-3 was decreased in HCC tissue, compared to adjacent normal tissues, and CIDE-3 expression and HCC differentiation were positively correlated. CIDE-3 expression levels were lower in poorly differentiated HCC tissue than in well-differentiated HCC tissue. Overexpressed CIDE-3 inhibited proliferation and induced apoptosis in HCC cells. We found that lipopolysaccharide-induced tumor necrosis factor (LITAF) interacted with CIDE-3 in hepatic cells. This is the first demonstrated interaction between CIDE-3 and LITAF, and the first report that CIDE-3 induces apoptosis in hepatocellular carcinoma.
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Affiliation(s)
- Jie Min
- State Key Laboratory Of Cancer Biology, Department of pathology, Xijing Hospital, The Fourth Military Medical University, 710032 Xi'an, China
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Identification and Characterization of a Novel Mouse Cidea N-terminal Truncated Isoform*. PROG BIOCHEM BIOPHYS 2010. [DOI: 10.3724/sp.j.1206.2010.00159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Matsubara S, Takahashi T, Kimura AP. Epigenetic patterns at the mouse prolyl oligopeptidase gene locus suggest the CpG island in the gene body to be a novel regulator for gene expression. Gene 2010; 465:17-29. [PMID: 20600704 DOI: 10.1016/j.gene.2010.06.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Revised: 06/16/2010] [Accepted: 06/17/2010] [Indexed: 10/19/2022]
Abstract
Prolyl oligopeptidase (POP) is a widely distributed serine peptidase which hydrolyzes small peptides on the carboxyl side of an internal proline residue. While its physiological role has been intensely studied, the regulatory mechanism of the gene expression is poorly understood. This time we assessed the POP mRNA expression in mouse embryos and tissues related to reproduction and development and found that POP mRNA was highly expressed in the ovarian granulosa cell, placental spongiotrophoblast, and blastocyst embryo. To elucidate the mechanism by which POP expression is regulated, we investigated DNA methylation and histone modification patterns of the two CpG islands (CGIs) found at the mouse POP locus. Whereas the CGI including the POP promoter (CGI-1) was completely hypomethylated in all the tissues examined, DNA methylation level of the CGI in the gene body (CGI-2) was lower in the granulosa cell, placenta, and blastocyst than in the liver. Some specific CpGs in CGI-2 were significantly demethylated in the three tissues. An in vitro reporter analysis indicated that CGI-2 enhanced POP promoter activity and its effect was significantly reduced by DNA methylation. Moreover, histone H3 acetylation and H3K4 methylation levels of CGI-2 were higher in the granulosa cell than liver. The results suggest that the CGI-2 region is a cis-element for the POP gene expression.
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Affiliation(s)
- Shin Matsubara
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
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Huang YW, Luo J, Weng YI, Mutch DG, Goodfellow PJ, Miller DS, Huang THM. Promoter hypermethylation of CIDEA, HAAO and RXFP3 associated with microsatellite instability in endometrial carcinomas. Gynecol Oncol 2010; 117:239-47. [PMID: 20211485 PMCID: PMC2849881 DOI: 10.1016/j.ygyno.2010.02.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2009] [Revised: 02/03/2010] [Accepted: 02/10/2010] [Indexed: 10/19/2022]
Abstract
OBJECTIVE DNA promoter methylation is an epigenetic phenomenon for long-term gene silencing during tumorigenesis. The purpose of this study is to identify novel hypermethylated loci associated with clinicopathologic variables in endometrioid endometrial carcinomas. METHODS To find hypermethylated promoter loci, we used differential methylation hybridization coupling with microarray and further validated by combined bisulfite restriction analysis and MassARRAY assay. Methylation levels of candidate loci were corrected with clinicopathologic factors of endometrial carcinomas. RESULTS Increased promoter methylation of CIDE, HAAO and RXFP3 was detected in endometrial carcinomas compared with adjacent normal tissues, and was associated with decreased gene expression of all three genes. In a clinical cohort, promoter hypermethylation on CIDEA, HAAO and RXFP3 was detected in 85, 63 and 71% of endometrial carcinomas, respectively (n=118, P<0.001) compared with uninvolved normal endometrium. Methylation status of CIDEA, HAAO and RXFP3 had significant association with microsatellite instability in tumors (P<0.001). Furthermore, methylation levels of HAAO were further found to relate to disease-free survivals (P=0.034). CONCLUSIONS Hypermethylation of CIDEA, HAAO and RXFP3 promoter regions appears to be a frequent event in endometrial carcinomas. Hypermethylation at these loci is strongly associated with microsatellite instability status. Moreover, HAAO methylation predicts disease-free survival in this cohort of patients with endometrioid endometrial cancer.
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Affiliation(s)
- Yi-Wen Huang
- Human Cancer Genetics Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Jingqin Luo
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Siteman Cancer Center, St. Louis, MO 63110, USA
| | - Yu-I Weng
- Human Cancer Genetics Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - David G. Mutch
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Siteman Cancer Center, St. Louis, MO 63110, USA
| | - Paul J. Goodfellow
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
- Siteman Cancer Center, St. Louis, MO 63110, USA
| | - David S. Miller
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tim H.-M. Huang
- Human Cancer Genetics Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
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Gao J, Song J, Huang H, Li Z, Du Y, Cao J, Li M, Lv S, Lin H, Gong Y. Methylation of the SPARC gene promoter and its clinical implication in pancreatic cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2010; 29:28. [PMID: 20338068 PMCID: PMC2862018 DOI: 10.1186/1756-9966-29-28] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Accepted: 03/26/2010] [Indexed: 12/20/2022]
Abstract
Background The secreted protein acidic and rich in cysteine (SPARC) plays a pivotal role in regulating cell-matrix interactions and tumor angiogenesis, proliferation, and migration. Detection of SPARC gene methylation may be useful as a tumorigenesis marker for early detection of pancreatic cancer. Methods Methylation of the SPARC gene transcriptional regulation region (TRR) was detected using bisulfite-specific (BSP) PCR-based sequencing analysis in 40 cases of pancreatic cancer and the adjacent normal tissues, 6 chronic pancreatitis tissues, and 6 normal pancreatic tissues. BSP cloning-based sequencing analysis was also performed in selected cases. Clinicopathological data from the cancer patients were collected and analyzed. Results Analysis of SPARC gene TRR methylation showed two hypermethylation wave peak regions: CpG Region 1 (CpG site 1-7) and CpG Region 2 (CpG site 8-12). Pancreatic tissues have shown methylation in both regions with gradual increases from normal, chronic pancreatitis, and adjacent normal tissues to cancerous tissues. However, Methylation of CpG Region 2 was more sensitive than CpG Region 1 in pancreatic tumorigenesis. Furthermore, the methylation level of CpG Region 2 was associated with increased tumor size and exposure to the risk factors (tobacco smoke and alcohol consumption) for developing pancreatic cancer. Conclusion Methylation of the SPARC gene, specifically CpG Region 2, may be an early event during pancreatic tumorigenesis and should be further evaluated as a tumorigenesis marker for early detection of pancreatic cancer.
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Affiliation(s)
- Jun Gao
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
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Identification of 5 novel genes methylated in breast and other epithelial cancers. Mol Cancer 2010; 9:51. [PMID: 20205715 PMCID: PMC2841122 DOI: 10.1186/1476-4598-9-51] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Accepted: 03/05/2010] [Indexed: 01/12/2023] Open
Abstract
Background There are several high throughput approaches to identify methylated genes in cancer. We utilized one such recently developed approach, MIRA (methylated-CpG island recovery assay) combined with CpG island arrays to identify novel genes that are epigenetically inactivated in breast cancer. Results Using this approach we identified numerous CpG islands that demonstrated aberrant DNA methylation in breast cancer cell lines. Using a combination of COBRA and sequencing of bisulphite modified DNA, we confirmed 5 novel genes frequently methylated in breast tumours; EMILIN2, SALL1, DBC1, FBLN2 and CIDE-A. Methylation frequencies ranged from between 25% and 63% in primary breast tumours, whilst matched normal breast tissue DNA was either unmethylated or demonstrated a much lower frequency of methylation compared to malignant breast tissue DNA. Furthermore expression of the above 5 genes was shown to be restored following treatment with a demethylating agent in methylated breast cancer cell lines. We have expanded this analysis across three other common epithelial cancers (lung, colorectal, prostate). We demonstrate that the above genes show varying levels of methylation in these cancers. Lastly and most importantly methylation of EMILIN2 was associated with poorer clinical outcome in breast cancer and was strongly associated with estrogen receptor as well as progesterone receptor positive breast cancers. Conclusion The combination of the MIRA assay with CpG island arrays is a very useful technique for identifying epigenetically inactivated genes in cancer genomes and can provide molecular markers for early cancer diagnosis, prognosis and epigenetic therapy.
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Visone T, Charron M, Wright WW. Activation and repression domains within the promoter of the rat cathepsin L gene orchestrate sertoli cell-specific and stage-specific gene transcription in transgenic mice. Biol Reprod 2009; 81:571-9. [PMID: 19458314 DOI: 10.1095/biolreprod.109.075952] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In murine testes, only Sertoli cells express the cathepsin L (Ctsl) gene, and this expression is restricted to stages V-VIII of the cycle. Our previous transgenic analysis of Tg (-2065/+977) demonstrated that this expression is regulated by a approximately 2-kb promoter. To begin to elucidate this regulation, we analyzed the in vivo expression of two new transgenes, Tg (-935/+977) and Tg (-451/+977). Tg (-935/+977) was expressed by Sertoli cells but, in contrast to Tg (-2065/+977), was expressed at all stages of the cycle, by spermatocytes, by the vascular endothelium, and by seven other organs. Tg (-451/+977) was not expressed by Sertoli cells but by spermatogenic cells and by the brain. Lack of expression of Tg (-451/+977) by Sertoli cells was not due to a lack of essential cis-acting elements. Transient transfection analysis of primary cultures of mature rat Sertoli cells demonstrated that in mature Sertoli cells, most of the activity of the Ctsl promoter is accounted for by one of two redundant upstream GC motifs and an Initiator that are within 100 bp of the transcription start site. We conclude that transcriptional repressors upstream from nucleotide -935 of the rat Ctsl gene restrict testicular expression of this gene to Sertoli cells at stages V-VIII. At these stages, transcriptional activators located between nucleotides -935 and -452 promote access of the transcriptional machinery to the two GC boxes and to the Initiator. Thus, upstream repressors and activators as well as cis-acting elements near the transcription start site control stage-specific Ctsl transcription by Sertoli cells.
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Affiliation(s)
- Thomas Visone
- Division of Reproductive Biology, Department of Biochemistry and Molecular Biology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
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Abstract
PURPOSE OF REVIEW The cell death-inducing DFF45-like effector (CIDE) family proteins, comprising three members, Cidea, Cideb, and Fsp27 (Cidec), have emerged as important regulators for various aspects of metabolism. This review summarizes our current understanding about the physiological roles of CIDE proteins, their transcriptional regulations, and their underlying mechanism in controlling the development of metabolic disorders. RECENT FINDINGS Animals with deficiency in Cidea, Cideb, and Fsp27 all display lean phenotypes with higher energy expenditure and are resistant to diet-induced obesity and insulin resistance. CIDE proteins, localized to lipid droplets and endoplasmic reticulum, control lipid metabolism in adipocytes and hepatocytes through regulating AMP-activated protein kinase stability and influencing lipogenesis or lipid droplet formation. The expression of CIDE proteins is controlled at both transcriptional and posttranslational levels and positively correlates with the development of obesity, liver steatosis, and insulin sensitivity in both rodents and humans. SUMMARY CIDE proteins are important regulators of energy homeostasis and are closely linked to the development of metabolic disorders including obesity, diabetes, and liver steatosis. They may serve as potential molecular targets for the screening of therapeutic drugs for these diseases.
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Affiliation(s)
- Jingyi Gong
- Protein Science Laboratory of Ministry of Education, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing, China
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Kim YJ, Cho SY, Yun CH, Moon YS, Lee TR, Kim SH. Transcriptional activation of Cidec by PPARgamma2 in adipocyte. Biochem Biophys Res Commun 2008; 377:297-302. [PMID: 18845124 DOI: 10.1016/j.bbrc.2008.09.129] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Accepted: 09/29/2008] [Indexed: 01/16/2023]
Abstract
Cidec is a lipid droplet-associated protein, which inhibits lipolysis, leading to the accumulation of triglycerides in adipocytes. However, the transcriptional regulation of Cidec in adipocyte remains unknown. In the present study we investigated that the mouse Cidec transcript is regulated by PPARgamma2. After the differentiation of adipocyte, the expression pattern of Cidec was similar to that of PPARgamma2. In the presence of a PPARgamma agonist, the level of Cidec mRNA was highly increased. In addition, putative PPRE sites were identified in the Cidec promoter. By chromatin immunoprecipitation assay and reporter assay, we observed the binding of PPARgamma2 to the promoter of Cidec. Gel shift assay and the mutagenesis study were showed that the -219/-207 region of the Cidec promoter could function as a PPRE of the Cidec promoter. These results suggest that PPARgamma2 is required for the transcriptional activity of Cidec during adipogenesis, which could be contributed to understand the molecular mechanism of lipid droplet formation in adipocytes.
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Affiliation(s)
- Yoon-Jin Kim
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea
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Csepregi A, Röcken C, Hoffmann J, Gu P, Saliger S, Müller O, Schneider-Stock R, Kutzner N, Roessner A, Malfertheiner P, Ebert MPA. APC promoter methylation and protein expression in hepatocellular carcinoma. J Cancer Res Clin Oncol 2007; 15:1415-28. [PMID: 20629990 PMCID: PMC4373337 DOI: 10.1111/j.1582-4934.2010.01124.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
PURPOSE We investigated the impact of promoter methylation on APC protein expression in patients with hepatocellular carcinoma (HCC). MATERIALS AND METHODS 50 patients [HCC (n=19), liver metastasis (n=19), cholangiocellular cancer (n=7), and benign liver tumors (n=5)] were studied for methylation using Methylight analysis. APC mutation was investigated by protein truncation test and direct sequencing of genomic DNA. The protein expression was evaluated by immunohistochemistry and Western blot analysis. RESULTS The APC promoter was hypermethylated in 81.8% of non-cancerous liver tissue samples. All HCC samples and ten patients with liver metastasis (52.6%) exhibited APC promoter methylation. The degree of methylation was significantly higher in samples from HCC compared to the non-cancerous liver tissue samples (63.1% vs. 24.98%; p=0.001). The level of APC protein expression was significantly reduced in HCC samples compared to that of the corresponding non-tumor liver tissue (p<0.05). CONCLUSIONS Promoter methylation of the APC gene seems to be of significance in hepatocarcinogenesis and results in reduced protein expression in HCC. Interestingly, APC promoter methylation is also present in the vast majority of non-cancerous liver tissue whose (patho)physiological function remains unresolved.
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Affiliation(s)
- Antal Csepregi
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Otto-von-Guericke University, Leipziger Strasse 44, 39120 Magdeburg, Germany.
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