1
|
Zong W, Wang Y, Zhang L, Lu W, Li W, Wang F, Cheng J. DNA Methylation Mediates Sperm Quality via piwil1 and piwil2 Regulation in Japanese Flounder ( Paralichthys olivaceus). Int J Mol Sci 2024; 25:5935. [PMID: 38892123 PMCID: PMC11172970 DOI: 10.3390/ijms25115935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/26/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
DNA methylation is an important way to regulate gene expression in eukaryotes. In order to reveal the role of DNA methylation in the regulation of germ cell-specific piwi gene expression during spermatogenesis of Japanese flounder (Paralichthys olivaceus), the expression profiles of piwil1 (piwi-like 1) and piwil2 (piwi-like 2) genes in the gonads of female, male, and sex-reversed pseudo-male P. olivaceus were analyzed, and the dynamic of DNA methylation was investigated. As a result, piwil1 and piwil2 genes were highly expressed in the testis of both male and pseudo-male P. olivaceus, with significant variation among male individuals. The DNA methylation levels in the promoter regions of both piwil1 and piwil2 were negatively correlated with their expression levels, which may contribute to the transcriptional regulation of piwi genes during spermatogenesis. There was also sperm quality variation among male P. olivaceus, and the sperm curvilinear velocity was positively correlated with the expression of both piwil1 and piwil2 genes. These results indicated that the DNA methylation in piwil1 and piwil2 promoter regions may affect the initiation of piwi gene transcription, thereby regulating gene expression and further affecting the spermatogenesis process and gamete quality in P. olivaceus.
Collapse
Affiliation(s)
- Wenyu Zong
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yapeng Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Lingqun Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Wei Lu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Weigang Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Fengchi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Jie Cheng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572024, China
- Laboratory for Marine Fisheries Science and Food Production Processes, National Laboratory for Marine Science and Technology, Qingdao 266237, China
| |
Collapse
|
2
|
Zhang Y, Chen J, Zheng B, Teng J, Lou Z, Feng H, Zhao S, Xue L. Genome-wide identification, evolution of DNA methyltransferases and their expression under salinity stress in Larimichthys crocea. Int J Biol Macromol 2024; 264:130603. [PMID: 38447841 DOI: 10.1016/j.ijbiomac.2024.130603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/08/2024] [Accepted: 02/24/2024] [Indexed: 03/08/2024]
Abstract
DNA methyltransferases (Dnmts) are responsible for DNA methylation which influences patterns of gene expression and plays a crucial role in response to environmental changes. In this study, 7 LcDnmt genes were identified in the genome of large yellow croaker (Larimichthys crocea). The comprehensive analysis was conducted on gene structure, protein and location site of LcDnmts. LcDnmt proteins belonged to three groups (Dnmt1, Dnmt2, and Dnmt3) according to their conserved domains and phylogenetic analysis. Although Dnmt3 can be further divided into three sub groups (Dnmt3a, Dnmt3b, and Dnmt3l), there is no Dnmnt3l member in the large yellow croaker. Phylogenetic analysis revealed that the Dnmt family was highly conserved in teleosts. Expression patterns derived from the RNA-seq, qRT-PCR and Western blot analysis revealed that 2 LcDnmt genes (LcDnmt1 and LcDnmt3a2) significantly regulated under salinity stress in the liver, which was found to be dominantly expressed in the intestine and brain, respectively. These two genes may play an important role in the salinity stress of large yellow croaker and represent candidates for future functional analysis. Our results revealed the conservation of Dnmts during evolution and indicated a potential role of Dnmts in epigenetic regulation of response to salinity stress.
Collapse
Affiliation(s)
- Yu Zhang
- School of Fishery, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China
| | - Jiaqian Chen
- School of Fishery, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China
| | - Baoxiao Zheng
- College of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315832, China
| | - Jian Teng
- School of Agricultural Science and Engineering, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Zhengjia Lou
- College of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315832, China
| | - Huijie Feng
- College of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315832, China
| | - Shiqi Zhao
- School of Fishery, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China.
| | - Liangyi Xue
- College of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315832, China.
| |
Collapse
|
3
|
Yu L, Gao Z, Li Z, Liu P, Gao Y, Liang G. Identification of ferroptosis-related molecular subtypes and a methylation-related ferroptosis gene prognostic signature in cervical squamous cell carcinoma. J Cancer Res Clin Oncol 2023; 149:14673-14689. [PMID: 37584713 DOI: 10.1007/s00432-023-05267-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/09/2023] [Indexed: 08/17/2023]
Abstract
PURPOSE We aimed to investigate the molecular characteristics of cervical squamous cell carcinoma (CESC) by analyzing ferroptosis-related gene (FRG) expression data to predict prognosis. METHODS Gene expression and clinicopathological data of patients with CESC were collected from the Cancer Genome Atlas and the Genotype-Tissue Expression databases. Using Cox regression analysis, we identified 21 FRGs associated with prognosis. Cluster analysis categorized patients into subgroups based on these genes and compared their clinicopathological, biological, and immune infiltration features. FRG methylation levels were examined, and a risk model based on such FRG methylation levels was constructed using LASSO and Cox regression analyses. The model's predictive capacity was validated, and the relationships between the risk score and immune infiltration, tumor microenvironment, and drug sensitivity were explored. FRG methylation in CESC tissues was validated by immunohistochemistry. RESULTS We identified 21 FRGs associated with CESC prognosis. Patients were stratified into two subtypes based on these genes, they showed differences in prognosis, immune cell types, and immune checkpoint expression. A three-gene risk score (including AQP3, MGST1, and TFRC) was generated, and the low-risk group showed better overall survival. The high-risk and low-risk groups differed in terms of immune infiltration, gene mutations, and drug sensitivity. Experimental validation confirmed the upregulation of AQP3 and TFRC, whereas MGST1 expression was not significantly altered in CESC tissues compared with that in normal cervical tissues. CONCLUSION This study highlights the potential role of FRG methylation in predicting CESC prognosis and provides a personalized assessment of immune responses in patients with CESC.
Collapse
Affiliation(s)
- Lijun Yu
- Department of Gynecology, Nanfang Hospital, Southern Medical University, No. 1838, Guang Zhou Northern Avenue, Guangzhou, 510515, China
- Department of Gynecology, First Hospital of Shanxi Medical University, No. 85 Jiefang South Road, Taiyuan, 030001, shanxi, China
| | - Zhenwei Gao
- Department of Gynecology, Nanfang Hospital, Southern Medical University, No. 1838, Guang Zhou Northern Avenue, Guangzhou, 510515, China
| | - Zeyu Li
- Shanxi Medical University, No. 56 Xinjian South Road, Taiyuan, 030001, shanxi, China
| | - Ping Liu
- Department of Gynecology, Nanfang Hospital, Southern Medical University, No. 1838, Guang Zhou Northern Avenue, Guangzhou, 510515, China.
| | - Ya Gao
- Department of Gynecology, First Hospital of Shanxi Medical University, No. 85 Jiefang South Road, Taiyuan, 030001, shanxi, China
| | - Gang Liang
- Department of Pathology, First Hospital of Shanxi Medical University, No. 85 Jiefang South Road, Taiyuan, 030001, shanxi, China
| |
Collapse
|
4
|
Su J, Yi S, Gao Z, Abbas K, Zhou X. DNA methylation mediates gonadal development via regulating the expression levels of cyp19a1a in loach Misgurnus anguillicaudatus. Int J Biol Macromol 2023; 235:123794. [PMID: 36828090 DOI: 10.1016/j.ijbiomac.2023.123794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023]
Abstract
DNA methylation-mediated transcriptional regulation has been considered to significantly impact some steroidogenic enzyme genes expression. To uncover the roles of DNA methylation on the regulation of aromatase gene expression during gametogenesis in Misgurnus anguillicaudatus, the expression profiles and cellular localization of cyp19a1a and cyp19a1b were analyzed, and the landscape of DNA methylation dynamics was investigated. We found that cyp19a1a was predominantly expressed in granulosa cells of oocytes, while cyp19a1b expression was enriched in radial glial cells of the forebrain. In ovary, cyp19a1a was highly expressed until the vitellogenesis stage. The average methylation levels, especially for two CpG sites within the cAMP response element, were negatively correlated with cyp19a1a expression levels, indicating that methylation could regulate cyp19a1a transcriptional activity by modulating the binding efficiency of cAMP to its response elements. Compared with in ovary, cyp19a1a showed lower expression in testis but was hypermethylated. Cyp19a1b in female brain weakly expressed before the vitellogenesis stage, but significantly elevated at the maturation stage. In both sexes, it maintained high methylation levels in brain despite the obvious fluctuation of the cyp19a1b expression. This study revealed that DNA methylation plays a key role in establishing cyp19a1a spatiotemporal expression patterns and thus mediates gonadal development in teleosts.
Collapse
Affiliation(s)
- Junxiao Su
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
| | - Shaokui Yi
- College of Life Sciences, Huzhou University, Huzhou 313000, China.
| | - Zexia Gao
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
| | - Khalid Abbas
- Aquaculture Biotechnology Lab, Department of Zoology, Wildlife and Fisheries, University of Agriculture, Faisalabad, Pakistan.
| | - Xiaoyun Zhou
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
| |
Collapse
|
5
|
Zhuo MQ, Chen J, Wu ML, Wang WB. Novel insights for PI3KC3 in mediating lipid accumulation in yellow catfish Pelteobagrus fulvidraco. FISH PHYSIOLOGY AND BIOCHEMISTRY 2022; 48:571-583. [PMID: 35389126 DOI: 10.1007/s10695-022-01071-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
In this study, the transcriptional regulation of PI3KC3 by three transcription factors (PPARγ, PPARα, and STAT3) and the potential role of PI3KC3 in mediating lipid accumulation were determined in yellow catfish Pelteobagrus fulvidraco. The 5'-deletion assay, overexpression assay, site-mutation assay, and electrophoretic mobility shift assay suggested that PPARα, PPARγ, and STAT3 negatively regulated the promoter activity of pi3kc3. Moreover, the transcriptional inactivation of pi3kc3 was directly mediated by PPARα and PPARγ under fatty acid (FA) treatment. Using primary hepatocytes from yellow catfish, FA incubation significantly increased triacylglyceride (TG) content, non-esterified fatty acid (NEFA) content, and lipid drops (LDs) content, the mRNA level of pparα, pparγ, stat3, and dnmt3b, the protein level of PPARα, PPARγ, and STAT3, and the methylation level of pi3kc3, but significantly reduced the mRNA and protein level of PI3KC3. Our findings offer new insights into the mechanisms for transcriptional regulation of PI3KC3 and for PI3KC3-mediated lipid accumulation in fish.
Collapse
Affiliation(s)
- Mei-Qin Zhuo
- School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, 430070, China.
| | - Jun Chen
- School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, 430070, China
| | - Mei-Li Wu
- School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, 430070, China
| | - Wen-Biao Wang
- School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, 430070, China
| |
Collapse
|
6
|
Zhu L, Li Y, Xia F, Xue M, Wang Y, Jia D, Gao Y, Li L, Shi Y, Chen S, Xu G, Yuan C. H19: A vital long noncoding RNA in the treatment of diabetes and diabetic complications. Curr Pharm Des 2021; 28:1011-1018. [PMID: 34895118 DOI: 10.2174/1381612827666211210123959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 10/29/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Increasing academic efforts have been made to explore the correlation of long noncoding RNAs (lncRNAs) with human diseases, particularly metabolic diseases like diabetes mellitus. Taking lncRNA H19 as an example, this review intends to reveal the functions and mechanism of lncRNA H19 in diabetes mellitus and diabetic complications. METHODS The research results associated with lncRNA H19 and diabetes mellitus are collected and summarized on PubMed. CONCLUSION LncRNA H19 is a potential instructive marker for the treatment of diabetes mellitus and diabetic complications.
Collapse
Affiliation(s)
- Leiqi Zhu
- College of Medical Science, China Three Gorges University, Yichang 443002. China
| | - Yuanyang Li
- College of Medical Science, China Three Gorges University, Yichang 443002. China
| | - Fangqi Xia
- College of Medical Science, China Three Gorges University, Yichang 443002. China
| | - Mengzhen Xue
- College of Medical Science, China Three Gorges University, Yichang 443002. China
| | - Yaqi Wang
- College of Medical Science, China Three Gorges University, Yichang 443002. China
| | - Dengke Jia
- College of Medical Science, China Three Gorges University, Yichang 443002. China
| | - Yan Gao
- College of Medical Science, China Three Gorges University, Yichang 443002. China
| | - Luoying Li
- College of Medical Science, China Three Gorges University, Yichang 443002. China
| | - Yue Shi
- College of Medical Science, China Three Gorges University, Yichang 443002. China
| | - Silong Chen
- College of Medical Science, China Three Gorges University, Yichang 443002. China
| | - Guangfu Xu
- College of Medical Science, China Three Gorges University, Yichang 443002. China
| | - Chengfu Yuan
- College of Medical Science, China Three Gorges University, Yichang 443002. China
| |
Collapse
|
7
|
Zhao Q, Wang W, Li JX, Yuan P, Liu Y, Li Y, Wang L, Song L. The DNA cytosine-5-methyltransferase 3 (DNMT3) involved in regulation of CgIL-17 expression in the immune response of oyster Crassostrea gigas. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 123:104092. [PMID: 33819545 DOI: 10.1016/j.dci.2021.104092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/29/2021] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
DNA methyltransferase, a key enzyme mediating DNA methylation, is involved in numerous processes including genomic imprinting, X chromosome inactivation, transposable element suppression, and immune defense in vertebrates. In the present study, a DNA cytosine-5-methyltransferase 3 was identified from oyster Crassostrea gigas (designed as CgDNMT3). There were a PWWP domain, a PHD domain and a DNA-methylase domain in the deduced amino acid sequences of CgDNMT3, and the conserved motifs I, IV, VI, Ⅷ, IX and X were identified in its C-terminal catalytic DNA-methylase domain. The mRNA transcripts of CgDNMT3 were detected in haemocytes, mantle, gill, adductor muscle, digestive gland and labial palp, with higher expression level in haemocytes (6.54 folds of those in gill, p < 0.01). The expression level of CgDNMT3 mRNA in haemocytes increased significantly after LPS primed (2.87 folds of that in control group, p < 0.05) in vitro or Vibrio splendidus challenging (1.94 folds of that in control group, p < 0.05) in vivo. Immunocytochemical analysis revealed that CgDNMT3 protein was distributed mainly in cytoplasm and partial in nucleus of oyster haemocytes. After CgDNMT3 was transfected and expressed in HEK293T cells, the DNA 5-methylcytosine (5-mc) level in the transfected group was significantly increased, which was 1.22 folds (p < 0.05) of the pcDNA-3.1 group. The expressions of oyster CgIL17-1, CgIL17-2 and CgIL17-5 in haemocytes increased (13.05 folds, 4.78 folds and 9.41 folds of that in control group, respectively) at 12 h after V. splendidus challenging, but the increase were significantly inhibited when the oysters were pre-treated with DNA methyltransferase inhibitor 5-Azacytidine, which were 9 folds, 1.93 folds and 3.22 folds of that in control group, respectively. These results collectively suggested that CgDNMT3 was a conserved member of DNA methyltransferase 3 family in oyster, and participated in regulating the expression of cytokines during immune response.
Collapse
Affiliation(s)
- Qi Zhao
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Weilin Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Jia Xin Li
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Pei Yuan
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Yu Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Yan Li
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China.
| |
Collapse
|
8
|
Balasubramaniyam T, Oh KI, Jin HS, Ahn HB, Kim BS, Lee JH. Non-Canonical Helical Structure of Nucleic Acids Containing Base-Modified Nucleotides. Int J Mol Sci 2021; 22:9552. [PMID: 34502459 PMCID: PMC8430589 DOI: 10.3390/ijms22179552] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 12/12/2022] Open
Abstract
Chemically modified nucleobases are thought to be important for therapeutic purposes as well as diagnosing genetic diseases and have been widely involved in research fields such as molecular biology and biochemical studies. Many artificially modified nucleobases, such as methyl, halogen, and aryl modifications of purines at the C8 position and pyrimidines at the C5 position, are widely studied for their biological functions. DNA containing these modified nucleobases can form non-canonical helical structures such as Z-DNA, G-quadruplex, i-motif, and triplex. This review summarizes the synthesis of chemically modified nucleotides: (i) methylation, bromination, and arylation of purine at the C8 position and (ii) methylation, bromination, and arylation of pyrimidine at the C5 position. Additionally, we introduce the non-canonical structures of nucleic acids containing these modifications.
Collapse
Affiliation(s)
- Thananjeyan Balasubramaniyam
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Kwnag-Im Oh
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Ho-Seong Jin
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
| | - Hye-Bin Ahn
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
| | - Byeong-Seon Kim
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
- Department of Chemistry Education, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Joon-Hwa Lee
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| |
Collapse
|
9
|
Evaluation of Methylation Profiles of An Epidermal Growth Factor Receptor Gene in a Head and Neck Squamous Cell Carcinoma Patient Group. Balkan J Med Genet 2021; 23:65-72. [PMID: 33816074 PMCID: PMC8009575 DOI: 10.2478/bjmg-2020-0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Upregulation of the epidermal growth factor receptor (EGFR) gene has shown an important impact on the development of head and neck cancers due to its important regulation role on multiple cell signaling pathways. The aim of this study was to investigate the methylation pattern of the promoter region of the EGFR gene between head and neck squamous cell carcinoma (HNSCC) patients and a control group. Forty-seven unrelated HNSCC patients, clinically diagnosed at the Department of Otorhinolaryngology, Dışkapı Yıldırım Beyazıt Training and Research Hospital, Ankara, Turkey, and 48 unrelated healthy volunteers from different geographic regions of Turkey, were included in this study. Methylation status of the promoter region of the EGFR gene was detected by methylation-specific-polymerase chain reaction (MS-PCR). The correlation between EGFR gene promoter methylation profiles and clinical characteristics were examined using the χ2 test. Methylation was observed in 79.0% of HNSCC patients, whereas this ratio was 90.0% in healthy individuals. The results show that promoter region methylation of the EGFR gene was not associated with HNSCC development in the studied Turkish patient group. In addition, the methylation status of the EGFR gene promoter was not found to be related to age, gender or tumor stage.
Collapse
|
10
|
Xu YH, Xu YC, Hogstrand C, Zhao T, Wu LX, Zhuo MQ, Luo Z. Waterborne copper exposure up-regulated lipid deposition through the methylation of GRP78 and PGC1α of grass carp Ctenopharyngodon idella. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 205:111089. [PMID: 32810645 DOI: 10.1016/j.ecoenv.2020.111089] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/05/2020] [Accepted: 07/27/2020] [Indexed: 06/11/2023]
Abstract
Early molecular events after the exposure of heavy metals, such as aberrant DNA methylation, suggest that DNA methylation was important in regulating physiological processes for animals and accordingly could be used as environmental biomarkers. In the present study, we found that copper (Cu) exposure increased lipid content and induced the DNA hypermethylation at the whole genome level. Especially, Cu induced hypermethylation of glucose-regulated protein 78 (grp78) and peroxisome proliferator-activated receptor gamma coactivator-1α (pgc1α). CCAAT/enhancer binding protein α (C/EBPα) could bind to the methylated sequence of grp78, whereas C/EBPβ could not bind to the methylated sequence of grp78. These synergistically influenced grp78 expression and increased lipogenesis. In contrast, DNA methylation of PGC1α blocked the specific protein 1 (SP1) binding and interfered mitochondrial function. Moreover, Cu increased reactive oxygen species (ROS) production, activated endoplasmic reticulum (ER) stress and damaged mitochondrial function, and accordingly increased lipid deposition. Notably, we found a new toxicological mechanism for Cu-induced lipid deposition at DNA methylation level. The measurement of DNA methylation facilitated the use of these epigenetic biomarkers for the evaluation of environmental risk.
Collapse
Affiliation(s)
- Yi-Huan Xu
- Laboratory of Molecular Nutrition and Environmental Toxicology for Aquatic Economic Animals, Fishery College, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yi-Chuang Xu
- Laboratory of Molecular Nutrition and Environmental Toxicology for Aquatic Economic Animals, Fishery College, Huazhong Agricultural University, Wuhan, 430070, China
| | - Christer Hogstrand
- Diabetes and Nutritional Sciences Division, School of Medicine, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Tao Zhao
- Laboratory of Molecular Nutrition and Environmental Toxicology for Aquatic Economic Animals, Fishery College, Huazhong Agricultural University, Wuhan, 430070, China
| | - Li-Xiang Wu
- Laboratory of Molecular Nutrition and Environmental Toxicology for Aquatic Economic Animals, Fishery College, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mei-Qin Zhuo
- Laboratory of Molecular Nutrition and Environmental Toxicology for Aquatic Economic Animals, Fishery College, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhi Luo
- Laboratory of Molecular Nutrition and Environmental Toxicology for Aquatic Economic Animals, Fishery College, Huazhong Agricultural University, Wuhan, 430070, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| |
Collapse
|
11
|
Sato S, Mukai Y. Modulation of Chronic Inflammation by Quercetin: The Beneficial Effects on Obesity. J Inflamm Res 2020; 13:421-431. [PMID: 32848440 PMCID: PMC7425105 DOI: 10.2147/jir.s228361] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/22/2020] [Indexed: 12/18/2022] Open
Abstract
Obesity has become a major risk factor for the development of chronic diseases such as insulin resistance, type 2 diabetes mellitus, and cardiovascular disease. Moreover, obesity induces chronic inflammation in adipose tissue, liver, skeletal muscle, and the vascular system. Quercetin is the major representative of the flavonoid subclass of flavonols, which is ubiquitously contained within natural plants such as green tea, and vegetables, including onions and apples. Researchers have focused greater attention to the beneficial physiological roles of quercetin, which has anti-oxidative, anti-inflammatory, and anti-fibrotic effects on insulin resistance and atherosclerosis in obesity-related diseases. Also, the anti-inflammatory effects of quercetin on intestinal microbiota have been demonstrated in obesity. In addition, there is increasing evidence that quercetin is associated with epigenetic activities in cancer, and in maternal undernutrition during gestation and lactation. In this review, we focus on the chemical properties of quercetin, its dietary sources in obesity, and its anti-inflammatory effects on insulin resistance, atherosclerosis, intestinal microbiota, and maternal under-nutrition with epigenetic activity.
Collapse
Affiliation(s)
- Shin Sato
- Department of Nutrition, Aomori University of Health and Welfare, Aomori 030-8505, Japan
| | - Yuuka Mukai
- School of Nutrition and Dietetics, Faculty of Health and Social Work, Kanagawa University of Human Services, Kanagawa 238-8522, Japan
| |
Collapse
|
12
|
Chen F, Liu X, Chen Y, Liu JY, Lu H, Wang W, Lu X, Dean KC, Gao L, Kaplan HJ, Dean DC, Peng X, Liu Y. Sphere-induced reprogramming of RPE cells into dual-potential RPE stem-like cells. EBioMedicine 2020; 52:102618. [PMID: 31982829 PMCID: PMC6994567 DOI: 10.1016/j.ebiom.2019.102618] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 11/20/2019] [Accepted: 12/18/2019] [Indexed: 12/11/2022] Open
Abstract
Background The retinal pigment epithelium (RPE) has the potential to regenerate the entire neuroretina upon retinal injury in amphibians. In contrast, this regenerative capacity has been lost in mammals. The reprogramming of differentiated somatic cells into induced pluripotent stem cells (iPSCs) by viral transduction of exogenous stem cell factors has triggered a revolution in regenerative medicine. However, the risks of potential mutation(s) caused by random viral vector insertion in host genomes and tumor formation in recipients hamper its clinical application. One alternative is to immortalize adult stem cells with limited potential or to partially reprogram differentiated somatic cells into progenitor-like cells through non-integration protocols. Methods Sphere-induced RPE stem cells (iRPESCs) were generated from adult mouse RPE cells. Their stem cell functionality was studied in a mouse model of retinal degeneration. The molecular mechanism underlying the sphere-induced reprogramming was investigated using microarray and loss-of-function approaches. Findings We provide evidence that our sphere-induced reprogramming protocol can immortalize and transform mouse RPE cells into iRPESCs with dual potential to differentiate into cells that express either RPE or photoreceptor markers both in vitro and in vivo. When subretinally transplanted into mice with retinal degeneration, iRPESCs can integrate to the RPE and neuroretina, thereby delaying retinal degeneration in the model animals. Our molecular analyses indicate that the Hippo signaling pathway is important in iRPESC reprogramming. Interpretation The Hippo factor Yap1 is activated in the nuclei of cells at the borders of spheres. The factors Zeb1 and P300 downstream of the Hippo pathway are shown to bind to the promoters of the stemness genes Oct4, Klf4 and Sox2, thereby likely transactivate them to reprogram RPE cells into iRPESCs. Fund National Natural Science Foundation of China and the National Institute of Health USA.
Collapse
Affiliation(s)
- Fenghua Chen
- Department of Ophthalmology and Visual Sciences, University of Louisville School of Medicine, 301 E Muhammad Ali Blvd, Louisville, Kentucky 40202, USA; Department of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing 100005, China
| | - Xiao Liu
- Department of Ophthalmology and Visual Sciences, University of Louisville School of Medicine, 301 E Muhammad Ali Blvd, Louisville, Kentucky 40202, USA; Department of Ophthalmology, Second Affiliated Hospital of Xiangya Medical School, Central South University, Changsha, China
| | - Yao Chen
- Department of Ophthalmology and Visual Sciences, University of Louisville School of Medicine, 301 E Muhammad Ali Blvd, Louisville, Kentucky 40202, USA; Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China
| | - John Y Liu
- Department of Ophthalmology and Visual Sciences, University of Louisville School of Medicine, 301 E Muhammad Ali Blvd, Louisville, Kentucky 40202, USA
| | - Huayi Lu
- Department of Ophthalmology and Visual Sciences, University of Louisville School of Medicine, 301 E Muhammad Ali Blvd, Louisville, Kentucky 40202, USA; Second Hospital of Jilin University, Changchun, Jilin Province, China
| | - Wei Wang
- Department of Ophthalmology and Visual Sciences, University of Louisville School of Medicine, 301 E Muhammad Ali Blvd, Louisville, Kentucky 40202, USA
| | - Xiaoqin Lu
- Department of Ophthalmology and Visual Sciences, University of Louisville School of Medicine, 301 E Muhammad Ali Blvd, Louisville, Kentucky 40202, USA
| | - Kevin C Dean
- Department of Ophthalmology and Visual Sciences, University of Louisville School of Medicine, 301 E Muhammad Ali Blvd, Louisville, Kentucky 40202, USA
| | - Ling Gao
- Department of Ophthalmology, Second Affiliated Hospital of Xiangya Medical School, Central South University, Changsha, China
| | - Henry J Kaplan
- Department of Ophthalmology and Visual Sciences, University of Louisville School of Medicine, 301 E Muhammad Ali Blvd, Louisville, Kentucky 40202, USA
| | - Douglas C Dean
- Department of Ophthalmology and Visual Sciences, University of Louisville School of Medicine, 301 E Muhammad Ali Blvd, Louisville, Kentucky 40202, USA; James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, Kentucky 40202, USA; Birth Defects Center; University of Louisville School of Medicine, Louisville, Kentucky 40202, USA.
| | - Xiaoyan Peng
- Department of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing 100005, China.
| | - Yongqing Liu
- Department of Ophthalmology and Visual Sciences, University of Louisville School of Medicine, 301 E Muhammad Ali Blvd, Louisville, Kentucky 40202, USA; James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, Kentucky 40202, USA; Birth Defects Center; University of Louisville School of Medicine, Louisville, Kentucky 40202, USA.
| |
Collapse
|
13
|
Wang FL, Yan LX, Shi HJ, Liu XY, Zheng QY, Sun LN, Wang DS. Genome-wide identification, evolution of DNA methyltransferases and their expression during gonadal development in Nile tilapia. Comp Biochem Physiol B Biochem Mol Biol 2018; 226:73-84. [PMID: 30170023 DOI: 10.1016/j.cbpb.2018.08.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/20/2018] [Accepted: 08/21/2018] [Indexed: 11/18/2022]
Abstract
DNA methyltransferases (dnmts) are responsible for DNA methylation and play important roles in organism development. In this study, seven dnmts genes (dnmt1, dnmt2, dnmt3aa, dnmt3ab, dnmt3ba, dnmt3bb.1, dnmt3bb.2) were identified in Nile tilapia. Comprehensive analyses of dnmts were performed using available genome databases from representative animal species. Phylogenetic analysis revealed that the dnmts family were highly conserved in teleosts. Based on transcriptome data from eight adult tilapia tissues, the dnmts were found to be dominantly expressed in the head kidney, testis and ovary. Analyses of the gonadal transcriptome data in different developmental stages revealed that all dnmts were expressed in both ovary and testis, and four de novo dnmts (dnmt3aa, dnmt3ab, dnmt3bb.1, dnmt3bb.2) showed higher expression in the testis than in the ovary. Furthermore, during sex reversal induced by Fadrozole, the expression of these four de novo dnmts increased significantly in treated group compared to female control group. By in situ hybridization, the seven dnmts were found to be expressed mainly in phase I and II oocytes of the ovary and spermatocytes of the testis. When gonads were incubated with a methyltransferase inhibitor (5-AzaCdR) in vitro, the expression of dnmts genes were down-regulated significantly, while the expression of cyp19a1a (a key gene in female pathway) and dmrt1 (a key gene in male pathway) increased significantly. Our results revealed the conservation of dnmts during evolution and indicated a potential role of dnmts in epigenetic regulation of gonadal development.
Collapse
Affiliation(s)
- Fei-Long Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China
| | - Long-Xia Yan
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China
| | - Hong-Juan Shi
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China
| | - Xing-Yong Liu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China
| | - Qiao-Yuan Zheng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China
| | - Li-Na Sun
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China.
| | - De-Shou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China.
| |
Collapse
|
14
|
Li J, Diao B, Guo S, Huang X, Yang C, Feng Z, Yan W, Ning Q, Zheng L, Chen Y, Wu Y. VSIG4 inhibits proinflammatory macrophage activation by reprogramming mitochondrial pyruvate metabolism. Nat Commun 2017; 8:1322. [PMID: 29109438 PMCID: PMC5673889 DOI: 10.1038/s41467-017-01327-4] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 09/11/2017] [Indexed: 01/24/2023] Open
Abstract
Exacerbation of macrophage-mediated inflammation contributes to pathogenesis of various inflammatory diseases, but the immunometabolic programs underlying regulation of macrophage activation are unclear. Here we show that V-set immunoglobulin-domain-containing 4 (VSIG4), a B7 family-related protein that is expressed by resting macrophages, inhibits macrophage activation in response to lipopolysaccharide. Vsig4 -/- mice are susceptible to high-fat diet-caused obesity and murine hepatitis virus strain-3 (MHV-3)-induced fulminant hepatitis due to excessive macrophage-dependent inflammation. VSIG4 activates the PI3K/Akt-STAT3 pathway, leading to pyruvate dehydrogenase kinase-2 (PDK2) upregulation and subsequent phosphorylation of pyruvate dehydrogenase, which results in reduction in pyruvate/acetyl-CoA conversion, mitochondrial reactive oxygen species secretion, and macrophage inhibition. Conversely, interruption of Vsig4 or Pdk2 promotes inflammation. Forced expression of Vsig4 in mice ameliorates MHV-3-induced viral fulminant hepatitis. These data show that VSIG4 negatively regulates macrophage activation by reprogramming mitochondrial pyruvate metabolism.
Collapse
Affiliation(s)
- Jialin Li
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, 400038, China
| | - Bo Diao
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, 400038, China
| | - Sheng Guo
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, 400038, China
| | - Xiaoyong Huang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, 400038, China
| | - Chengying Yang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, 400038, China
| | - Zeqing Feng
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, 400038, China
| | - Weiming Yan
- Institute of Infectious Disease, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Qin Ning
- Institute of Infectious Disease, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Lixin Zheng
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, MD, 20892, USA
| | - Yongwen Chen
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, 400038, China.
| | - Yuzhang Wu
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, 400038, China.
| |
Collapse
|
15
|
Transgenerational pancreatic impairment with Igf2/H19 epigenetic alteration induced by p,p'-DDE exposure in early life. Toxicol Lett 2017; 280:222-231. [PMID: 28867213 DOI: 10.1016/j.toxlet.2017.08.083] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 08/24/2017] [Accepted: 08/24/2017] [Indexed: 02/06/2023]
Abstract
The hypothesis of fetal origins indicates that exposures in early development could induce epigenetic modifications in the male germ-line, affecting the susceptibility of adult-onset disease for generations. p,p'-DDE, the primary metabolite of persistent organochlorine pesticide DDT, is highly correlated with impaired glucose tolerance (IGT) and a strong contributing factor to type 2 diabetes. In our previous study, ancestral p,p'-DDE exposure could induce transgenerational impaired male fertility with sperm Igf2 hypomethylation. It is still unknown whether this germline epigenetic defect would affect the somatic tissue endocrine pancreas. Gestating F0 generation females were exposed to p,p'-DDE from gestation day 8 to 15. The F1 male offspring were mated with female to produce F2 progeny. F3 generation was obtained by intercrossing the control and treated male and female of F2 generation and divided as C♂-C♀, DDE♂-DDE♀, DDE♂-C♀ and C♂-DDE♀. Results indicated that F1 offspring in p,p'-DDE group exhibited impaired glucose tolerance (IGT), abnormal insulin secretion, β-cell dysfunction and altered Igf2 and H19 expression induced by Igf2/H19 hypomethylation, which could be transferred to the F3 offspring through the male germ line. IGT and abnormal insulin secretion were more obvious in males than those in females. Ancestral p,p'-DDE exposure could induce transgenerational pancreatic impairment with Igf2/H19 epigenetic defect.
Collapse
|
16
|
McCullough LE, Chen J, Cho YH, Khankari NK, Bradshaw PT, White AJ, Teitelbaum SL, Terry MB, Neugut AI, Hibshoosh H, Santella RM, Gammon MD. Modification of the association between recreational physical activity and survival after breast cancer by promoter methylation in breast cancer-related genes. Breast Cancer Res 2017; 19:19. [PMID: 28222775 PMCID: PMC5319077 DOI: 10.1186/s13058-017-0811-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/01/2017] [Indexed: 12/22/2022] Open
Abstract
Background Mechanisms underlying the inverse association between physical activity and survival after breast cancer are unresolved, but DNA methylation may play a role. We hypothesized that promoter methylation of breast cancer-related genes, as well as global methylation, may modify the association between prediagnostic recreational physical activity (RPA) and breast cancer mortality. Methods Using a population-based sample of 1254 women diagnosed with first primary breast cancer, we examined modification of the RPA-mortality association by gene-specific promoter methylation and global methylation. Average lifetime RPA was assessed from menarche to diagnosis through structured in-home interviews. Promoter methylation of 13 breast cancer-related genes was evaluated in archived tumor by methylation-specific polymerase chain reaction and MethyLight assay. Global methylation in white blood cell DNA was determined at long interspersed nucleotide element 1 and by the luminometric methylation assay. After approximately 15 years of follow-up, 486 patients had died, and 186 of the deaths were breast cancer-related. We used Cox proportional hazards regression to estimate HRs and 95% CIs as well as likelihood ratio tests to assess multiplicative interactions. Results All-cause mortality was lower only among physically active women with methylated promoter of APC (HR 0.60, 95% CI 0.40–0.80), CCND2 (HR 0.56, 95% CI 0.32–0.99), HIN (HR 0.55, 95% CI 0.38–0.80), and TWIST1 (HR 0.28, 95% CI 0.14–0.56) in tumors, but not among those with unmethylated tumors (significant interaction p < 0.05). We found no interaction between RPA and global methylation. Conclusions The improved survival after breast cancer that is associated with RPA may be more pronounced in women with promoter tumor methylation in biologically plausible genes. Electronic supplementary material The online version of this article (doi:10.1186/s13058-017-0811-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | - Jia Chen
- Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Oncological Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yoon Hee Cho
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Nikhil K Khankari
- Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
| | - Patrick T Bradshaw
- Division of Epidemiology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Alexandra J White
- Epidemiology Branch, National Institute of Environmental Health Science, Research Triangle Park, NC, 27709, USA
| | - Susan L Teitelbaum
- Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Mary Beth Terry
- Department of Epidemiology, Columbia University, New York, NY, 10032, USA
| | - Alfred I Neugut
- Department of Epidemiology, Columbia University, New York, NY, 10032, USA.,Department of Medicine, Columbia University, New York, NY, 10032, USA
| | - Hanina Hibshoosh
- Department of Pathology, Columbia University, New York, NY, 10032, USA
| | - Regina M Santella
- Department of Environmental Health Sciences, Columbia University, New York, NY, 10032, USA
| | - Marilie D Gammon
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| |
Collapse
|
17
|
Maternal High Estradiol Exposure is Associated with Elevated Thyroxine and Pax8 in Mouse Offspring. Sci Rep 2016; 6:36805. [PMID: 27827435 PMCID: PMC5101534 DOI: 10.1038/srep36805] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 10/21/2016] [Indexed: 01/26/2023] Open
Abstract
Our previous studies have shown that maternal high estradiol (E2) environment increased the risk of thyroid dysfunction in offspring. However, the mechanism involved remains unexplored. To evaluate the thyroid function of offspring after high E2 exposure and to explore the underlying mechanism, we established a high E2 mouse model of early pregnancy, and detected thyroid hormones of their offspring. In thyroids of offspring, the expressions of Tg, Nis, Tpo, Pax8, and Titf1 and CpG island methylation status of Pax8 and genes involved in methylation were analyzed. We found that thyroxine (T4) and FT4 levels of offspring were obviously increased in the high-E2 group, especially in females. In both 3- and 8-week-old offspring of the high-E2 group, Pax8 was significantly up-regulated in thyroid glands, accompanied by the abnormal CpG island methylation status in the promoter region. Furthermore, Dnmt3a and Mbd1 were obviously down-regulated in thyroids of the high E2 group. Besides, the disturbance of thyroid function in females was more severe than that in males, implying that the effects were related to gender. In summary, our study indicated that maternal high E2 exposure disturbed the thyroid function of offspring through the dysregulation and abnormal DNA methylation of Pax8.
Collapse
|
18
|
Kitchen MO, Bryan RT, Emes RD, Glossop JR, Luscombe C, Cheng KK, Zeegers MP, James ND, Devall AJ, Mein CA, Gommersall L, Fryer AA, Farrell WE. Quantitative genome-wide methylation analysis of high-grade non-muscle invasive bladder cancer. Epigenetics 2016; 11:237-46. [PMID: 26929985 DOI: 10.1080/15592294.2016.1154246] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
High-grade non-muscle invasive bladder cancer (HG-NMIBC) is a clinically unpredictable disease with greater risks of recurrence and progression relative to their low-intermediate-grade counterparts. The molecular events, including those affecting the epigenome, that characterize this disease entity in the context of tumor development, recurrence, and progression, are incompletely understood. We therefore interrogated genome-wide DNA methylation using HumanMethylation450 BeadChip arrays in 21 primary HG-NMIBC tumors relative to normal bladder controls. Using strict inclusion-exclusion criteria we identified 1,057 hypermethylated CpGs within gene promoter-associated CpG islands, representing 256 genes. We validated the array data by bisulphite pyrosequencing and examined 25 array-identified candidate genes in an independent cohort of 30 HG-NMIBC and 18 low-intermediate-grade NMIBC. These analyses revealed significantly higher methylation frequencies in high-grade tumors relative to low-intermediate-grade tumors for the ATP5G2, IRX1 and VAX2 genes (P<0.05), and similarly significant increases in mean levels of methylation in high-grade tumors for the ATP5G2, VAX2, INSRR, PRDM14, VSX1, TFAP2b, PRRX1, and HIST1H4F genes (P<0.05). Although inappropriate promoter methylation was not invariantly associated with reduced transcript expression, a significant association was apparent for the ARHGEF4, PON3, STAT5a, and VAX2 gene transcripts (P<0.05). Herein, we present the first genome-wide DNA methylation analysis in a unique HG-NMIBC cohort, showing extensive and discrete methylation changes relative to normal bladder and low-intermediate-grade tumors. The genes we identified hold significant potential as targets for novel therapeutic intervention either alone, or in combination, with more conventional therapeutic options in the treatment of this clinically unpredictable disease.
Collapse
Affiliation(s)
- Mark O Kitchen
- a Institute for Science and Technology in Medicine, Keele University , UK.,b Urology Department , University Hospitals of North Midlands NHS Trust , UK
| | - Richard T Bryan
- c Institute of Cancer and Genomic Sciences, University of Birmingham , UK
| | - Richard D Emes
- d Advanced Data Analysis Center, University of Nottingham , UK
| | - John R Glossop
- a Institute for Science and Technology in Medicine, Keele University , UK
| | | | - K K Cheng
- c Institute of Cancer and Genomic Sciences, University of Birmingham , UK
| | - Maurice P Zeegers
- c Institute of Cancer and Genomic Sciences, University of Birmingham , UK.,e Department of Complex Genetics , Maastricht University Medical Center , The Netherlands.,f NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center , The Netherlands.,g CAPHRI School for Public Health and Primary Care, Maastricht University Medical Center , The Netherlands
| | | | - Adam J Devall
- c Institute of Cancer and Genomic Sciences, University of Birmingham , UK
| | - Charles A Mein
- i The Genome Center, Barts and the London School of Medicine and Dentistry , London , UK
| | - Lyndon Gommersall
- b Urology Department , University Hospitals of North Midlands NHS Trust , UK
| | - Anthony A Fryer
- a Institute for Science and Technology in Medicine, Keele University , UK
| | - William E Farrell
- a Institute for Science and Technology in Medicine, Keele University , UK
| |
Collapse
|
19
|
Chen HP, Zhao YT, Zhao TC. Histone deacetylases and mechanisms of regulation of gene expression. Crit Rev Oncog 2015; 20:35-47. [PMID: 25746103 DOI: 10.1615/critrevoncog.2015012997] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In recent years it has become widely recognized that histone modification plays a pivotal role in controlling gene expression and is involved in a wide spectrum of disease regulation. Histone acetylation is a major modification that affects gene transcription and is controlled by histone acetyltransferases (HATs) and histone deacetylases (HDACs). HATs acetylate lysines of histone proteins, resulting in the relaxation of chromatin structure, and they also facilitate gene activation. Conversely, HDACs remove acetyl groups from hyperacetylated histones and suppress general gene transcription. In addition to histones, numerous nonhistone proteins can be acetylated and deacetylated, and they also are involved in the regulation of a wide range of diseases. To date there are 18 HDACs in mammals classified into 4 classes based on homology to yeast HDACs. Accumulating evidence has revealed that HDACs play crucial roles in a variety of biological processes including inflammation, cell proliferation, apoptosis, and carcinogenesis. In this review we summarize the current state of knowledge of HDACs in carcinogenesis and describe the involvement of HDACs in cancer-associated molecular processes. It is hoped than an understanding of the role of HDACs in cancer will lead to the design of more potent and specific drugs targeting selective HDAC proteins for the treatment of the disease.
Collapse
Affiliation(s)
- Hong Ping Chen
- Department of Surgery, Boston University Medical School, Boston University, Roger Williams Medical Center, Providence, RI; Department of Histology and Embryology, Medical College, Nanchang University, Nanchang, China
| | - Yu Tina Zhao
- Department of Surgery, Boston University Medical School, Boston University, Roger Williams Medical Center, Providence, RI
| | - Ting C Zhao
- Department of Surgery, Boston University Medical School, Boston University, Roger Williams Medical Center, Providence, RI
| |
Collapse
|
20
|
Moen EL, Mariani CJ, Zullow H, Jeff-Eke M, Litwin E, Nikitas JN, Godley LA. New themes in the biological functions of 5-methylcytosine and 5-hydroxymethylcytosine. Immunol Rev 2015; 263:36-49. [PMID: 25510270 DOI: 10.1111/imr.12242] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) play a critical role in development and normal physiology. Alterations in 5-mC and 5-hmC patterns are common events in hematopoietic neoplasms. In this review, we begin by emphasizing the importance of 5-mC, 5-hmC, and their enzymatic modifiers in hematological malignancies. Then, we discuss the functions of 5-mC and 5-hmC at distinct genic contexts, including promoter regions, gene bodies, intron-exon boundaries, alternative promoters, and intragenic microRNAs. Recent advances in technology have allowed for the study of 5-mC and 5-hmC independently and specifically permitting distinction between the bases that show them to have transcriptional effects that vary by their location relative to gene structure. We extend these observations to their functions at enhancers and transcription factor binding sites. We discuss dietary influences on 5-mC and 5-hmC levels and summarize the literature on the effects of folate and vitamin C on 5-mC and 5-hmC, respectively. Finally, we discuss how these new themes in the functions of 5-mC and 5-hmC will likely influence the broader research field of epigenetics.
Collapse
Affiliation(s)
- Erika L Moen
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, USA; Committee on Cancer Biology, The University of Chicago, Chicago, IL, USA
| | | | | | | | | | | | | |
Collapse
|
21
|
Duncan HF, Smith AJ, Fleming GJP, Cooper PR. Epigenetic modulation of dental pulp stem cells: implications for regenerative endodontics. Int Endod J 2015; 49:431-46. [PMID: 26011759 DOI: 10.1111/iej.12475] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 05/24/2015] [Indexed: 12/28/2022]
Abstract
Dental pulp stem cells (DPSCs) offer significant potential for use in regenerative endodontics, and therefore, identifying cellular regulators that control stem cell fate is critical to devising novel treatment strategies. Stem cell lineage commitment and differentiation are regulated by an intricate range of host and environmental factors of which epigenetic influence is considered vital. Epigenetic modification of DNA and DNA-associated histone proteins has been demonstrated to control cell phenotype and regulate the renewal and pluripotency of stem cell populations. The activities of the nuclear enzymes, histone deacetylases, are increasingly being recognized as potential targets for pharmacologically inducing stem cell differentiation and dedifferentiation. Depending on cell maturity and niche in vitro, low concentration histone deacetylase inhibitor (HDACi) application can promote dedifferentiation of several post-natal and mouse embryonic stem cell populations and conversely increase differentiation and accelerate mineralization in DPSC populations, whilst animal studies have shown an HDACi-induced increase in stem cell marker expression during organ regeneration. Notably, both HDAC and DNA methyltransferase inhibitors have also been demonstrated to dramatically increase the reprogramming of somatic cells to induced pluripotent stem cells (iPSCs) for use in regenerative therapeutic procedures. As the regulation of cell fate will likely remain the subject of intense future research activity, this review aims to describe the current knowledge relating to stem cell epigenetic modification, focusing on the role of HDACi on alteration of DPSC phenotype, whilst presenting the potential for therapeutic application as part of regenerative endodontic regimens.
Collapse
Affiliation(s)
- H F Duncan
- Division of Restorative Dentistry & Periodontology, Dublin Dental University Hospital, Trinity College, Dublin, Ireland
| | - A J Smith
- Oral Biology, School of Dentistry, University of Birmingham, Birmingham, UK
| | - G J P Fleming
- Material Science Unit, Dublin Dental University Hospital, Trinity College, Dublin, Ireland
| | - P R Cooper
- Oral Biology, School of Dentistry, University of Birmingham, Birmingham, UK
| |
Collapse
|
22
|
Wu LX, Wen CJ, Li Y, Zhang X, Shao YY, Yang Z, Zhou HH. Interindividual epigenetic variation in ABCB1 promoter and its relationship with ABCB1 expression and function in healthy Chinese subjects. Br J Clin Pharmacol 2015; 80:1109-21. [PMID: 25940551 DOI: 10.1111/bcp.12675] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 04/25/2015] [Accepted: 04/30/2015] [Indexed: 12/15/2022] Open
Abstract
AIM Interindividual epigenetic variation is likely to be an important mechanism contributing to the interindividual variability in the expression and function of ATP-binding cassette, sub-family B, member 1 (ABCB1). The aim of the present study was to explore the effect of interindividual epigenetic variability in the ABCB1 promoter on ABCB1 expression and function in healthy Chinese subjects. METHODS Using bisulfite sequencing polymerase chain reaction (PCR) and chromatin immunoprecipitation assays, the DNA methylation and histone acetylation status of the ABCB1 promoter in stool DNA and exfoliated colonic epithelial cells of 157 healthy Chinese male volunteers was analysed. ABCB1 mRNA levels in colonic epithelial cells were detected by real-time PCR. The digoxin pharmacokinetics in subjects with different epigenetic profiles was investigated after a single oral administration of digoxin (0.5 mg). RESULTS The methylation levels of ABCB1 promoter in stool DNA showed a significant interindividual variation, from 0.84% to 18.05%. A high methylation level of the ABCB1 promoter was closely related to the low levels of acetylated histone H3 and ABCB1 mRNA expression. In the high methylation group, the area under the concentration-time curves (AUC(0-4 h) and AUC(0-10 h) ) of digoxin was increased by 19% [95% confidence interval (CI) 10%, 31%; P = 0.024] and 13% (95% CI 8%, 26%; P = 0.026), respectively, and the peak concentration (Cmax ) of digoxin was increased by 30% (95% CI 12%, 41%; P = 0.021) compared with the low methylation group. CONCLUSIONS The epigenetic modifications of the ABCB1 promoter show high interindividual variability in healthy Chinese subjects, and are closely related to the interindividual variation in ABCB1 mRNA expression and digoxin 0-4 h plasma concentrations in vivo.
Collapse
Affiliation(s)
- Lan-Xiang Wu
- Institute of life sciences, Chongqing Medical University, Chongqing, P.R. China
| | - Chun-Jie Wen
- Institute of life sciences, Chongqing Medical University, Chongqing, P.R. China
| | - Ying Li
- Institute of life sciences, Chongqing Medical University, Chongqing, P.R. China
| | - Xue Zhang
- Institute of life sciences, Chongqing Medical University, Chongqing, P.R. China
| | - Ying-Ying Shao
- Institute of life sciences, Chongqing Medical University, Chongqing, P.R. China
| | - Zhu Yang
- Institute of life sciences, Chongqing Medical University, Chongqing, P.R. China
| | - Hong-Hao Zhou
- Institute of life sciences, Chongqing Medical University, Chongqing, P.R. China.,Pharmacogenetics Research Institute, Institute of Clinical Pharmacology, Central South University, Changsha, Hunan, P.R. China
| |
Collapse
|
23
|
Kaku M, Yamauchi M. Mechano-regulation of collagen biosynthesis in periodontal ligament. J Prosthodont Res 2014; 58:193-207. [PMID: 25311991 DOI: 10.1016/j.jpor.2014.08.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 08/25/2014] [Indexed: 12/12/2022]
Abstract
Periodontal ligament (PDL) plays critical roles in the development and maintenance of periodontium such as tooth eruption and dissipation of masticatory force. The mechanical properties of PDL are mainly derived from fibrillar type I collagen, the most abundant extracellular component. The biosynthesis of type I collagen is a long, complex process including a number of intra- and extracellular post-translational modifications. The final modification step is the formation of covalent intra- and intermolecular cross-links that provide collagen fibrils with stability and connectivity. It is now clear that collagen post-translational modifications are regulated by groups of specific enzymes and associated molecules in a tissue-specific manner; and these modifications appear to change in response to mechanical force. This review focuses on the effect of mechanical loading on collagen biosynthesis and fibrillogenesis in PDL with emphasis on the post-translational modifications of collagens, which is an important molecular aspect to understand in the field of prosthetic dentistry.
Collapse
Affiliation(s)
- Masaru Kaku
- Division of Bioprosthodontics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.
| | - Mitsuo Yamauchi
- North Carolina Oral Health Institute, University of North Carolina at Chapel Hill, NC, USA
| |
Collapse
|
24
|
Friemel C, Ammerpohl O, Gutwein J, Schmutzler AG, Caliebe A, Kautza M, von Otte S, Siebert R, Bens S. Array-based DNA methylation profiling in male infertility reveals allele-specific DNA methylation in PIWIL1 and PIWIL2. Fertil Steril 2014; 101:1097-1103.e1. [PMID: 24524831 DOI: 10.1016/j.fertnstert.2013.12.054] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 12/13/2013] [Accepted: 12/26/2013] [Indexed: 12/31/2022]
Abstract
OBJECTIVE To identify CpG sites differentially methylated in peripheral blood of men with idiopathic infertility due to impaired spermatogenesis as compared with fertile controls. DESIGN DNA methylation profiling on peripheral blood samples using the HumanMethylation450 BeadChip (Illumina) in patients and controls, single-nucleotide polymorphism (SNP) typing by Sanger sequencing. SETTING University institute in cooperation with genetic and infertility clinics. PATIENT(S) 30 infertile men with normal CFTR and AZF tests and karyotype, and 10 fertile male controls. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) DNA methylation levels at CpG sites. RESULT(S) We identified 471 CpGs (287 genes) as differentially methylated between patients and controls. These were significantly enriched for the gene ontology functions MHC class II receptor activity and piwi-interacting (piRNA) binding. The latter was associated with two methylation-sensitive SNPs in the genes PIWIL1 and PIWIL2, respectively, which showed significant allele distribution skewing in the infertile cohort. We found that 445 (94.5%) of 471 differentially methylated CpGs were associated with SNPs, but 26 (15 genes) were not genomically templated, including the ENO1, MTA2, BRSK2, and LBX2 genes previously associated with fertility and spermatogenesis. CONCLUSION(S) Our study identifies surrogate DNA methylation markers for idiopathic infertility in peripheral blood and suggests that allele-specific DNA methylation differences at regulatory sites of genes involved in piRNA regulation are associated with disturbed spermatogenesis.
Collapse
Affiliation(s)
- Carolin Friemel
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Ole Ammerpohl
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Jana Gutwein
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Andreas G Schmutzler
- Department of Gynecology and Obstetrics, Center of Reproductive Medicine, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Almuth Caliebe
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Monika Kautza
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Sören von Otte
- Department of Gynecology and Obstetrics, Center of Reproductive Medicine, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Susanne Bens
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.
| |
Collapse
|
25
|
Yu MH, Huang YC, Chang PL. Rapid screening of the heterogeneity of DNA methylation by single-strand conformation polymorphism and CE-LIF in the presence of electro-osmotic flow. Electrophoresis 2014; 35:2378-85. [DOI: 10.1002/elps.201300502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/14/2013] [Accepted: 12/16/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Meng-Hsuan Yu
- Department of Chemistry; Tunghai University; Taichung Taiwan
| | - Ya-Chi Huang
- Department of Chemistry; Tunghai University; Taichung Taiwan
| | - Po-Ling Chang
- Department of Chemistry; Tunghai University; Taichung Taiwan
| |
Collapse
|
26
|
Farmen E, Hultman MT, Anglès d'Auriac M, Tollefsen KE. Development of a screening system for the detection of chemically induced DNA methylation alterations in a zebrafish liver cell line. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2014; 77:587-599. [PMID: 24754394 DOI: 10.1080/15287394.2014.887423] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Early molecular events with correlation to disease, such as aberrant DNA methylation, emphasize the importance of DNA methylation as a potential environmental biomarker. Currently, little is known regarding how various environmental contaminants and mixtures alter DNA methylation in aquatic organisms, and testing is both time- and labor-consuming. Therefore, the potential of an in vitro screening method was evaluated by exposing zebrafish liver cells (ZF-L) for 96 h to the nonmutagenic model substance 5'-azacytidine (AZA), as well as a selection of environmental pollutants such as sodium arsenite (NAS), 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), 17α-ethinylestradiol (EE2), and diethylstilbestrol (DES). Six single genes with reported and anticipated importance in cancer were selected for analysis. Methylation of gene promoter areas was monitored by bisulfite conversion and high-resolution melt (HRM) analysis after exposure to sublethal concentrations of the test compounds. Subsequently, results were validated with direct bisulfite sequencing. Exposure of ZF-L cells to 0.5 μM AZA for 96 h led to hypomethylation of genes with both low and high basal methylation indicating similarity to mechanism of action in mammals. Further, NAS, EE2, and DES were shown to induce significant alterations in methylation, whereas TCDD did not. It was concluded that cell line exposure in combination with HRM may provide an initial contaminant screening assay by quantifying DNA methylation alterations with high throughput capacity. In addition, the rapid determination of effects following contaminant exposure with this in vitro system points to the possibility for new in vivo applications to be useful for environmental monitoring.
Collapse
Affiliation(s)
- Eivind Farmen
- a Norwegian Institute for Water Research , Oslo , Norway
| | | | | | | |
Collapse
|
27
|
Wen AY, You F, Sun P, Li J, Xu DD, Wu ZH, Ma DY, Zhang PJ. CpG methylation of dmrt1 and cyp19a promoters in relation to their sexual dimorphic expression in the Japanese flounder Paralichthys olivaceus. JOURNAL OF FISH BIOLOGY 2014; 84:193-205. [PMID: 24372528 DOI: 10.1111/jfb.12277] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Accepted: 10/11/2013] [Indexed: 06/03/2023]
Abstract
To better understand the effects of DNA methylation on the expression patterns of dmrt1 (Doublesex and Mab-3-related transcription factor 1) and cyp19a (Cytochrome P450 19a) in the Japanese flounder Paralichthys olivaceus, quantitative expressions, cellular distributions and cytosine-p-guanine (CpG) methylation patterns of these two genes in the gonads were analysed. The results showed that P. olivaceus dmrt1 expression was 70 times higher in the testis than in the ovary (P < 0·05). Its mRNA was detected clearly in spermatocytes and Sertoli cells of the testis, but weakly in the ovary. Paralichthys olivaceus cyp19a expression was 40 times higher in the ovary than in the testis (P < 0·01). Its mRNA was detected clearly in follicular cells of the ovary, but weakly in spermatocytes of the testis. The dmrt1 promoter CpGs were not methylated in the testis, whereas 57·69% were methylated in the ovary. For the cyp19a promoter CpGs, 97·5% were methylated in the testis and 73·33% were methylated in the ovary. These findings demonstrate that P. olivaceus dmrt1 and cyp19a are sex-related genes with sexual dimorphic expression, CpG methylation levels of the two genes are consistent with their expression quantities, and this epigenetic modification can influence the differential expression of genes in the gonads of P. olivaceus.
Collapse
Affiliation(s)
- A Y Wen
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, Shandong, People's Republic of China; College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | | | | | | | | | | | | | | |
Collapse
|
28
|
A Framework to Examine the Role of Epigenetics in Health Disparities among Native Americans. Nurs Res Pract 2013; 2013:410395. [PMID: 24386563 PMCID: PMC3872279 DOI: 10.1155/2013/410395] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 11/06/2013] [Accepted: 11/19/2013] [Indexed: 12/29/2022] Open
Abstract
Background. Native Americans disproportionately experience adverse childhood experiences (ACEs) as well as health disparities, including high rates of posttraumatic stress, depression, and substance abuse. Many ACEs have been linked to methylation changes in genes that regulate the stress response, suggesting that these molecular changes may underlie the risk for psychiatric disorders related to ACEs. Methods. We reviewed published studies to provide evidence that ACE-related methylation changes contribute to health disparities in Native Americans. This framework may be adapted to understand how ACEs may result in health disparities in other racial/ethnic groups. Findings. Here we provide evidence that links ACEs to methylation differences in genes that regulate the stress response. Psychiatric disorders are also associated with methylation differences in endocrine, immune, and neurotransmitter genes that serve to regulate the stress response and are linked to psychiatric symptoms and medical morbidity. We provide evidence linking ACEs to these epigenetic modifications, suggesting that ACEs contribute to the vulnerability for developing psychiatric disorders in Native Americans. Conclusion. Additional studies are needed to better understand how ACEs contribute to health and well-being. These studies may inform future interventions to address these serious risks and promote the health and well-being of Native Americans.
Collapse
|
29
|
Yu CE, Cudaback E, Foraker J, Thomson Z, Leong L, Lutz F, Gill JA, Saxton A, Kraemer B, Navas P, Keene CD, Montine T, Bekris LM. Epigenetic signature and enhancer activity of the human APOE gene. Hum Mol Genet 2013; 22:5036-47. [PMID: 23892237 DOI: 10.1093/hmg/ddt354] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The human apolipoprotein E (APOE) gene plays an important role in lipid metabolism. It has three common genetic variants, alleles ε2/ε3/ε4, which translate into three protein isoforms of apoE2, E3 and E4. These isoforms can differentially influence total serum cholesterol levels; therefore, APOE has been linked with cardiovascular disease. Additionally, its ε4 allele is strongly associated with the risk of Alzheimer's disease (AD), whereas the ε2 allele appears to have a modest protective effect for AD. Despite decades of research having illuminated multiple functional differences among the three apoE isoforms, the precise mechanisms through which different APOE alleles modify diseases risk remain incompletely understood. In this study, we examined the genomic structure of APOE in search for properties that may contribute novel biological consequences to the risk of disease. We identify one such element in the ε2/ε3/ε4 allele-carrying 3'-exon of APOE. We show that this exon is imbedded in a well-defined CpG island (CGI) that is highly methylated in the human postmortem brain. We demonstrate that this APOE CGI exhibits transcriptional enhancer/silencer activity. We provide evidence that this APOE CGI differentially modulates expression of genes at the APOE locus in a cell type-, DNA methylation- and ε2/ε3/ε4 allele-specific manner. These findings implicate a novel functional role for a 3'-exon CGI and support a modified mechanism of action for APOE in disease risk, involving not only the protein isoforms but also an epigenetically regulated transcriptional program at the APOE locus driven by the APOE CGI.
Collapse
Affiliation(s)
- Chang-En Yu
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA 98108, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Xi Z, Zinman L, Moreno D, Schymick J, Liang Y, Sato C, Zheng Y, Ghani M, Dib S, Keith J, Robertson J, Rogaeva E. Hypermethylation of the CpG island near the G4C2 repeat in ALS with a C9orf72 expansion. Am J Hum Genet 2013; 92:981-9. [PMID: 23731538 DOI: 10.1016/j.ajhg.2013.04.017] [Citation(s) in RCA: 207] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 04/05/2013] [Accepted: 04/22/2013] [Indexed: 12/13/2022] Open
Abstract
The G4C2 repeat expansion in C9orf72 is the most common known cause of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). We tested the hypothesis that the repeat expansion causes aberrant CpG methylation near the G4C2 repeat, which could be responsible for the downregulation of gene expression. We investigated the CpG methylation profile by two methods using genomic DNA from the blood of individuals with ALS (37 expansion carriers and 64 noncarriers), normal controls (n = 76), and family members of 7 ALS probands with the expansion. We report that hypermethylation of the CpG island 5' of the G4C2 repeat is associated with the presence of the expansion (p < 0.0001). A higher degree of methylation was significantly correlated with a shorter disease duration (p < 0.01), associated with familial ALS (p = 0.009) and segregated with the expansion in 7 investigated families. Notably, we did not detect methylation for either normal or intermediate alleles (up to 43 repeats), bringing to question the current cutoff of 30 repeats for pathological alleles. Our study raises several important questions for the future investigation of large data sets, such as whether the degree of methylation corresponds to clinical presentation (ALS versus FTLD).
Collapse
Affiliation(s)
- Zhengrui Xi
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, 6 Queen's Park Crescent West, Toronto, ON M5S 3H2, Canada
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Pan X, Chen Z, Huang R, Yao Y, Ma G. Transforming growth factor β1 induces the expression of collagen type I by DNA methylation in cardiac fibroblasts. PLoS One 2013; 8:e60335. [PMID: 23560091 PMCID: PMC3613378 DOI: 10.1371/journal.pone.0060335] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 02/25/2013] [Indexed: 11/18/2022] Open
Abstract
Transforming growth factor-beta (TGF-β), a key mediator of cardiac fibroblast activation, has a major influence on collagen type I production. However, the epigenetic mechanisms by which TGF-β induces collagen type I alpha 1 (COL1A1) expression are not fully understood. This study was designed to examine whether or not DNA methylation is involved in TGF-β-induced COL1A1 expression in cardiac fibroblasts. Cells isolated from neonatal Sprague-Dawley rats were cultured and stimulated with TGF-β1. The mRNA levels of COL1A1 and DNA methyltransferases (DNMTs) were determined via quantitative polymerase chain reaction and the protein levels of collagen type I were determined via Western blot as well as enzyme-linked immunosorbent assay. The quantitative methylation of the COL1A1 promoter region was analyzed using the MassARRAY platform of Sequenom. Results showed that TGF-β1 upregulated the mRNA expression of COL1A1 and induced the synthesis of cell-associated and secreted collagen type I in cardiac fibroblasts. DNMT1 and DNMT3a expressions were significantly downregulated and the global DNMT activity was inhibited when treated with 10 ng/mL of TGF-β1 for 48 h. TGF-β1 treatment resulted in a significant reduction of the DNA methylation percentage across multiple CpG sites in the rat COL1A1 promoter. Thus, TGF-β1 can induce collagen type I expression through the inhibition of DNMT1 and DNMT3a expressions as well as global DNMT activity, thereby resulting in DNA demethylation of the COL1A1 promoter. These findings suggested that the DNMT-mediated DNA methylation is an important mechanism in regulating the TGF-β1-induced COL1A1 gene expression.
Collapse
Affiliation(s)
- Xiaodong Pan
- Department of Cardiology, Zhongda Hospital, Medical School of Southeast University, Nanjing, Jiangsu, China
| | - Zhongpu Chen
- Department of Cardiology, Zhongda Hospital, Medical School of Southeast University, Nanjing, Jiangsu, China
| | - Rong Huang
- Department of Cardiology, Zhongda Hospital, Medical School of Southeast University, Nanjing, Jiangsu, China
| | - Yuyu Yao
- Department of Cardiology, Zhongda Hospital, Medical School of Southeast University, Nanjing, Jiangsu, China
| | - Genshan Ma
- Department of Cardiology, Zhongda Hospital, Medical School of Southeast University, Nanjing, Jiangsu, China
- * E-mail:
| |
Collapse
|
32
|
Guintivano J, Aryee MJ, Kaminsky ZA. A cell epigenotype specific model for the correction of brain cellular heterogeneity bias and its application to age, brain region and major depression. Epigenetics 2013; 8:290-302. [PMID: 23426267 PMCID: PMC3669121 DOI: 10.4161/epi.23924] [Citation(s) in RCA: 270] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Brain cellular heterogeneity may bias cell type specific DNA methylation patterns, influencing findings in psychiatric epigenetic studies. We performed fluorescence activated cell sorting (FACS) of neuronal nuclei and Illumina HM450 DNA methylation profiling in post mortem frontal cortex of 29 major depression and 29 matched controls. We identify genomic features and ontologies enriched for cell type specific epigenetic variation. Using the top cell epigenotype specific (CETS) marks, we generated a publically available R package, “CETS,” capable of quantifying neuronal proportions and generating in silico neuronal profiles from DNA methylation data. We demonstrate a significant overlap in major depression DNA methylation associations between FACS separated and CETS model generated neuronal profiles relative to bulk profiles. CETS derived neuronal proportions correlated significantly with age in the frontal cortex and cerebellum and accounted for epigenetic variation between brain regions. CETS based control of cellular heterogeneity will enable more robust hypothesis testing in the brain.
Collapse
Affiliation(s)
- Jerry Guintivano
- The Mood Disorders Center, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | | |
Collapse
|
33
|
Ma LL, Yi SH, Huang DX, Mei K, Yang RZ. Screening and identification of tissue-specific methylation for body fluid identification. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2013. [DOI: 10.1016/j.fsigss.2013.10.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
34
|
Reisner W, Pedersen JN, Austin RH. DNA confinement in nanochannels: physics and biological applications. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2012; 75:106601. [PMID: 22975868 DOI: 10.1088/0034-4885/75/10/106601] [Citation(s) in RCA: 246] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
DNA is the central storage molecule of genetic information in the cell, and reading that information is a central problem in biology. While sequencing technology has made enormous advances over the past decade, there is growing interest in platforms that can readout genetic information directly from long single DNA molecules, with the ultimate goal of single-cell, single-genome analysis. Such a capability would obviate the need for ensemble averaging over heterogeneous cellular populations and eliminate uncertainties introduced by cloning and molecular amplification steps (thus enabling direct assessment of the genome in its native state). In this review, we will discuss how the information contained in genomic-length single DNA molecules can be accessed via physical confinement in nanochannels. Due to self-avoidance interactions, DNA molecules will stretch out when confined in nanochannels, creating a linear unscrolling of the genome along the channel for analysis. We will first review the fundamental physics of DNA nanochannel confinement--including the effect of varying ionic strength--and then discuss recent applications of these systems to genomic mapping. Apart from the intense biological interest in extracting linear sequence information from elongated DNA molecules, from a physics view these systems are fascinating as they enable probing of single-molecule conformation in environments with dimensions that intersect key physical length-scales in the 1 nm to 100 µm range.
Collapse
Affiliation(s)
- Walter Reisner
- Physics Department, McGill University, Montreal QC, Canada.
| | | | | |
Collapse
|
35
|
Russo V, Bernabò N, Di Giacinto O, Martelli A, Mauro A, Berardinelli P, Curini V, Nardinocchi D, Mattioli M, Barboni B. H3K9 trimethylation precedes DNA methylation during sheep oogenesis: HDAC1, SUV39H1, G9a, HP1, and Dnmts are involved in these epigenetic events. J Histochem Cytochem 2012; 61:75-89. [PMID: 23019017 DOI: 10.1369/0022155412463923] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The oocyte, to become a fully mature gamete, has to acquire a correct pattern of DNA methylation on its genome; this epigenetic event represents the major point of the molecular mechanisms that occur during postnatal oogenesis. It is known that an intimate link exists between DNA methylation and histone posttranslational modifications, such as trimethylation of lysine 9 on histone 3 (H3K9me3), that is essential in the silencing of gene transcription. What remains unclear is the precise sequence of these two epigenetic events and the protein expression of the enzymes that catalyze this epigenetic maturation during oogenesis. To identify the key molecules involved in global DNA methylation and H3K9me3, a biological network-based computational model was realized. Then, the spatiotemporal distribution of the proteins, identified from the biological network, was assessed during postnatal oogenesis. The results obtained suggest the existence of a sequential cascade of events in which H3K9me3 is the primary step followed by DNA methylation. These two epigenetic marks are realized due to the recruitment of the HDAC1, SUV39H1, G9a, HP1, and Dnmt3a, which were always localized in the nuclei of the oocytes and were dependent on chromatin configuration. These results involving DNA methylation and H3K9me3 are crucial in defining the oocyte developmental competence.
Collapse
Affiliation(s)
- Valentina Russo
- Department of Comparative Biomedical Sciences, University of Teramo, Teramo, Italy.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Zeybel M, Hardy T, Wong YK, Mathers JC, Fox CR, Gackowska A, Oakley F, Burt AD, Wilson CL, Anstee QM, Barter MJ, Masson S, Elsharkawy AM, Mann DA, Mann J. Multigenerational epigenetic adaptation of the hepatic wound-healing response. Nat Med 2012; 18:1369-77. [PMID: 22941276 PMCID: PMC3489975 DOI: 10.1038/nm.2893] [Citation(s) in RCA: 202] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 07/02/2012] [Indexed: 02/06/2023]
Abstract
We investigated whether ancestral liver damage leads to heritable reprogramming of hepatic wound healing in male rats. We found that a history of liver damage corresponds with transmission of an epigenetic suppressive adaptation of the fibrogenic component of wound healing to the male F1 and F2 generations. Underlying this adaptation was less generation of liver myofibroblasts, higher hepatic expression of the antifibrogenic factor peroxisome proliferator-activated receptor γ (PPAR-γ) and lower expression of the profibrogenic factor transforming growth factor β1 (TGF-β1) compared to rats without this adaptation. Remodeling of DNA methylation and histone acetylation underpinned these alterations in gene expression. Sperm from rats with liver fibrosis were enriched for the histone variant H2A.Z and trimethylation of histone H3 at Lys27 (H3K27me3) at PPAR-γ chromatin. These modifications to the sperm chromatin were transmittable by adaptive serum transfer from fibrotic rats to naive rats and similar modifications were induced in mesenchymal stem cells exposed to conditioned media from cultured rat or human myofibroblasts. Thus, it is probable that a myofibroblast-secreted soluble factor stimulates heritable epigenetic signatures in sperm so that the resulting offspring better adapt to future fibrogenic hepatic insults. Adding possible relevance to humans, we found that people with mild liver fibrosis have hypomethylation of the PPARG promoter compared to others with severe fibrosis.
Collapse
Affiliation(s)
- Müjdat Zeybel
- Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Ding GL, Wang FF, Shu J, Tian S, Jiang Y, Zhang D, Wang N, Luo Q, Zhang Y, Jin F, Leung PC, Sheng JZ, Huang HF. Transgenerational glucose intolerance with Igf2/H19 epigenetic alterations in mouse islet induced by intrauterine hyperglycemia. Diabetes 2012; 61:1133-42. [PMID: 22447856 PMCID: PMC3331740 DOI: 10.2337/db11-1314] [Citation(s) in RCA: 201] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Gestational diabetes mellitus (GDM) has been shown to be associated with high risk of diabetes in offspring. However, the mechanisms involved and the possibilities of transgenerational transmission are still unclear. We intercrossed male and female adult control and first-generation offspring of GDM (F1-GDM) mice to obtain the second-generation (F2) offspring in four groups: C♂-C♀, C♂-GDM♀, GDM♂-C♀, and GDM♂-GDM♀. We found that birth weight significantly increased in F2 offspring through the paternal line with impaired glucose tolerance (IGT). Regardless of birth from F1-GDM with or without IGT, high risk of IGT appeared as early as 3 weeks in F2 offspring and progressed through both parental lineages, especial the paternal line. IGT in male offspring was more obvious than that in females, with parental characteristics and sex-specific transmission. In both F1 and F2 offspring of GDM, the expression of imprinted genes Igf2 and H19 was downregulated in pancreatic islets, caused by abnormal methylation status of the differentially methylated region, which may be one of the mechanisms for impaired islet ultrastructure and function. Furthermore, altered Igf2 and H19 gene expression was found in sperm of adult F1-GDM, regardless of the presence of IGT, indicating that changes of epigenetics in germ cells contributed to transgenerational transmission.
Collapse
Affiliation(s)
- Guo-Lian Ding
- Department of Reproductive Endocrinology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Fang-Fang Wang
- Department of Reproductive Endocrinology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jing Shu
- Department of Reproductive Endocrinology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Shen Tian
- Department of Reproductive Endocrinology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Ying Jiang
- Department of Reproductive Endocrinology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Dan Zhang
- Department of Reproductive Endocrinology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Ning Wang
- Department of Reproductive Endocrinology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Qiong Luo
- Department of Reproductive Endocrinology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yu Zhang
- Department of Reproductive Endocrinology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Fan Jin
- Department of Reproductive Endocrinology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Peter C.K. Leung
- Department of Obstetrics and Gynecology, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jian-Zhong Sheng
- Department of Pathophysiology, School of Medicine, Zhejiang University, Hangzhou, China
| | - He-Feng Huang
- Department of Reproductive Endocrinology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Reproductive Genetics, Ministry of Education, Hangzhou, China
- Corresponding author: He-Feng Huang, , or Jian-Zhong Sheng,
| |
Collapse
|
38
|
Urbán S V, Benevolenskaya E, Kiss J, Sági B, Hegyi B, Uher F. [Beyond genetics--the emerging role of epigenetics and its clinical aspects]. Orv Hetil 2012; 153:214-21. [PMID: 22296925 DOI: 10.1556/oh.2012.29301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Analysis of genomic sequences has clearly shown that the genomic differences among species do not explain the diversity of life. The genetic code itself serves as only a part of the dynamic complexity that results in the temporal and spatial changes in cell phenotypes during development. It has been concluded that the phenotype of a cell and of the organism as a whole is more influenced by environmentally-induced changes in gene activity than had been previously thought. The emerging field of epigenetics focuses on molecular marks on chromatin; called the epigenome, which serve as transmitters between the genome and the environment. These changes not only persist through multiple cell division cycles, but may also endure for multiple generations. Irregular alterations of the epigenome; called epimutations, may have a decisive role in the etiology of human pathologies such as malignancies and other complex human diseases. Epigenetics can provide the missing link between genetics, disease and the environment. Therefore, this field may have an increasing impact on future drug design and serve as a basis for new therapeutic/preventative approaches.
Collapse
|
39
|
Crea F, Paolicchi E, Marquez VE, Danesi R. Polycomb genes and cancer: time for clinical application? Crit Rev Oncol Hematol 2011; 83:184-93. [PMID: 22112692 DOI: 10.1016/j.critrevonc.2011.10.007] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 10/12/2011] [Accepted: 10/26/2011] [Indexed: 12/12/2022] Open
Abstract
Polycomb group genes (PcGs) are epigenetic effectors, essential for stem cell self-renewal and pluripotency. Two main Polycomb repressive complexes (PRC1, PRC2) mediate gene silencing through histone post-translational modifications. PcGs have been the focus of investigation in cancer research. Many cancer types show an over-expression of PcGs, predicting poor prognosis, metastasis and chemoresistance. Genetic polymorphisms of EZH2 (a PRC2 component) are significantly associated to lung cancer risk. Recently, 3-Deazaneplanocin A (DZNeP) was identified as an efficient inhibitor of PRC2 activity. DZNeP impairs cancer stem cell self-renewal and tumorigenicity. Despite the well-established role of PcGs in cancer stem cell biology, few studies dissected the clinical significance of these genes. In this paper, we explore PcGs as predictive and prognostic factors in oncology, with particular emphasis on what they can add to current biomarkers. We also propose a model for the rational development of DZNeP-based anticancer regimens and suggest the therapeutic applications of this drug.
Collapse
Affiliation(s)
- Francesco Crea
- Department of Internal Medicine, Division of Pharmacology, University of Pisa, Via Roma 55, 56100 Pisa, Italy.
| | | | | | | |
Collapse
|
40
|
Ilnytskyy Y, Kovalchuk O. Non-targeted radiation effects-an epigenetic connection. Mutat Res 2011; 714:113-25. [PMID: 21784089 DOI: 10.1016/j.mrfmmm.2011.06.014] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 06/24/2011] [Accepted: 06/29/2011] [Indexed: 01/18/2023]
Abstract
Ionizing radiation (IR) is a pivotal diagnostic and treatment modality, yet it is also a potent genotoxic agent that causes genome instability and carcinogenesis. While modern cancer radiation therapy has led to increased patient survival rates, the risk of radiation treatment-related complications is becoming a growing problem. IR-induced genome instability has been well-documented in directly exposed cells and organisms. It has also been observed in distant 'bystander' cells. Enigmatically, increased instability is even observed in progeny of pre-conceptually exposed animals, including humans. The mechanisms by which it arises remain obscure and, recently, they have been proposed to be epigenetic in nature. Three major epigenetic phenomena include DNA methylation, histone modifications and small RNA-mediated silencing. This review focuses on the role of DNA methylation and small RNAs in directly exposed and bystander tissues and in IR-induced transgenerational effects. Here, we present evidence that IR-mediated effects are maintained by epigenetic mechanisms.
Collapse
Affiliation(s)
- Yaroslav Ilnytskyy
- Department of Biological Sciences, University of Lethbridge, Lethbridge T1K 3M4, Alberta, Canada
| | | |
Collapse
|
41
|
Abstract
Acetylation of histone and non-histone proteins alters gene expression and induces a host of cellular effects. The acetylation process is homeostatically balanced by two groups of cellular enzymes, histone acetyltransferases (HATs) and histone deacetylases (HDACs). HAT activity relaxes the structure of the human chromatin, rendering it transcriptionally active, thereby increasing gene expression. In contrast, HDAC activity leads to gene silencing. The enzymatic balance can be ‘tipped’ by histone deacetylase inhibitors (HDACi), leading to an accumulation of acetylated proteins, which subsequently modify cellular processes including stem cell differentiation, cell cycle, apoptosis, gene expression, and angiogenesis. There is a variety of natural and synthetic HDACi available, and their pleiotropic effects have contributed to diverse clinical applications, not only in cancer but also in non-cancer areas, such as chronic inflammatory disease, bone engineering, and neurodegenerative disease. Indeed, it appears that HDACi-modulated effects may differ between ‘normal’ and transformed cells, particularly with regard to reactive oxygen species accumulation, apoptosis, proliferation, and cell cycle arrest. The potential beneficial effects of HDACi for health, resulting from their ability to regulate global gene expression by epigenetic modification of DNA-associated proteins, also offer potential for application within restorative dentistry, where they may promote dental tissue regeneration following pulpal damage.
Collapse
Affiliation(s)
- H.F. Duncan
- Division of Restorative Dentistry & Periodontology, Dublin Dental University Hospital, Trinity College Dublin, Lincoln Place, Dublin 2, Ireland
| | - A.J. Smith
- Oral Biology, School of Dentistry, University of Birmingham, St Chads Queensway, Birmingham, B4 6NN, UK
| | - G.J.P. Fleming
- Material Science Unit, Division of Oral Biosciences, Dublin Dental University Hospital, Trinity College Dublin, Lincoln Place, Dublin 2, Ireland
| | - P.R. Cooper
- Oral Biology, School of Dentistry, University of Birmingham, St Chads Queensway, Birmingham, B4 6NN, UK
| |
Collapse
|
42
|
Gigek CO, Lisboa LCF, Leal MF, Silva PNO, Lima EM, Khayat AS, Assumpção PP, Burbano RR, Smith MDAC. SMARCA5 methylation and expression in gastric cancer. Cancer Invest 2011; 29:162-6. [PMID: 21261476 DOI: 10.3109/07357907.2010.543365] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Here, we first evaluated SMARCA5 expression and promoter DNA methylation in gastric carcinogenesis. Immunohistochemistry and methylation-specific PCR were analyzed in 19 and 48 normal mucosa and in 52 and 92 gastric cancer samples, respectively. We observed higher immunoreactivity of SMARCA5 in gastric cancer samples than in normal mucosa. Moreover, SMARCA5 promoter methylation was associated with the absence of protein expression. Our findings suggest that SMARCA5 has a potential role in proliferation and malignancy in gastric carcinogenesis.
Collapse
Affiliation(s)
- Carolina Oliveira Gigek
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Sun WZ, Han GX. Detection of the promoter methylation status of the EDNRB gene in human gastric cancer cell line KATO III. Shijie Huaren Xiaohua Zazhi 2010; 18:3448-3451. [DOI: 10.11569/wcjd.v18.i32.3448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To detect the promoter methylation status and mRNA expression of the endothelin receptor type B (EDNRB) gene in human gastric cancer cell line KATO III and to analyze their clinical significance.
METHODS: Genomic DNA and total RNA were extracted from healthy adult peripheral blood samples and KATO III cells. Bisulfite sequencing PCR and reverse transcription-PCR were performed to analyze the promoter methylation status and mRNA expression of the EDNRB gene, respectively.
RESULTS: In KATO III cells, some CG loci (≤20%) were not or lowly methylated, while some others (≥50%) were hypermethylated. In healthy adult peripheral blood samples, only one CG locus (10%) was methylated, while the others were not methylated. The promoter methylation extent of the EDNRB gene in KATO III cells was higher than that in healthy adult peripheral blood samples. The mRNA expression was inhibited significantly in KATO III cells compared with healthy adult peripheral blood samples.
CONCLUSION: EDNRB gene promoter is hypermethylated in KATO III cells. The promoter methylation of the EDNRB gene may play an important role in the pathogenesis of gastric cancer.
Collapse
|
44
|
López Castel A, Nakamori M, Tomé S, Chitayat D, Gourdon G, Thornton CA, Pearson CE. Expanded CTG repeat demarcates a boundary for abnormal CpG methylation in myotonic dystrophy patient tissues. Hum Mol Genet 2010; 20:1-15. [PMID: 21044947 DOI: 10.1093/hmg/ddq427] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Myotonic dystrophy (DM1) affects multiple organs, shows age-dependent progression and is caused by CTG expansions at the DM1 locus. We determined the DM1 CpG methylation profile and CTG length in tissues from DM1 foetuses, DM1 adults, non-affected individuals and transgenic DM1 mice. Analysis included CTCF binding sites upstream and downstream of the CTG tract, as methylation-sensitive CTCF binding affects chromatinization and transcription of the DM1 locus. In humans, in a given foetus, expansions were largest in heart and smallest in liver, differing by 40-400 repeats; in adults, the largest expansions were in heart and cerebral cortex and smallest in cerebellum, differing by up to 5770 repeats in the same individual. Abnormal methylation was specific to the mutant allele. In DM1 adults, heart, liver and cortex showed high-to-moderate methylation levels, whereas cerebellum, kidney and skeletal muscle were devoid of methylation. Methylation decreased between foetuses and adults. Contrary to previous findings, methylation was not restricted to individuals with congenital DM1. The expanded repeat demarcates an abrupt boundary of methylation. Upstream sequences, including the CTCF site, were methylated, whereas the repeat itself and downstream sequences were not. In DM1 mice, expansion-, tissue- and age-specific methylation patterns were similar but not identical to those in DM1 individuals; notably in mice, methylation was present up- and downstream of the repeat, but greater upstream. Thus, in humans, the CpG-free expanded CTG repeat appears to maintain a highly polarized pattern of CpG methylation at the DM1 locus, which varies markedly with age and tissues.
Collapse
Affiliation(s)
- Arturo López Castel
- Genetics and Genome Biology, Department of Pediatrics, The Hospital for Sick Children, and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | | | | | | | | | | |
Collapse
|
45
|
Hoyo C, Murphy SK, Jirtle RL. Imprint regulatory elements as epigenetic biosensors of exposure in epidemiological studies. J Epidemiol Community Health 2010; 63:683-4. [PMID: 19679714 DOI: 10.1136/jech.2009.090803] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
46
|
Arnsdorf EJ, Tummala P, Castillo AB, Zhang F, Jacobs CR. The epigenetic mechanism of mechanically induced osteogenic differentiation. J Biomech 2010; 43:2881-6. [PMID: 20728889 DOI: 10.1016/j.jbiomech.2010.07.033] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 07/21/2010] [Indexed: 01/13/2023]
Abstract
Epigenetic regulation of gene expression occurs due to alterations in chromatin proteins that do not change DNA sequence, but alter the chromatin architecture and the accessibility of genes, resulting in changes to gene expression that are preserved during cell division. Through this process genes are switched on or off in a more durable fashion than other transient mechanisms of gene regulation, such as transcription factors. Thus, epigenetics is central to cellular differentiation and stem cell linage commitment. One such mechanism is DNA methylation, which is associated with gene silencing and is involved in a cell's progression towards a specific fate. Mechanical signals are a crucial regulator of stem cell behavior and important in tissue differentiation; however, there has been no demonstration of a mechanism whereby mechanics can affect gene regulation at the epigenetic level. In this study, we identified candidate DNA methylation sites in the promoter regions of three osteogenic genes from bone marrow derived mesenchymal stem cells (MSCs). We demonstrate that mechanical stimulation alters their epigenetic state by reducing DNA methylation and show an associated increase in expression. We contrast these results with biochemically induced differentiation and distinguish expression changes associated with durable epigenetic regulation from those likely to be due to transient changes in regulation. This is an important advance in stem cell mechanobiology as it is the first demonstration of a mechanism by which the mechanical micro-environment is able to induce epigenetic changes that control osteogenic cell fate, and that can be passed to daughter cells. This is a first step to understanding that will be vital to successful bone tissue engineering and regenerative medicine, where continued expression of a desired long-term phenotype is crucial.
Collapse
Affiliation(s)
- Emily J Arnsdorf
- Bone and Joint Rehabilitation R&D Center, VA Palo Alto Medical Center, Palo Alto, CA, United States
| | | | | | | | | |
Collapse
|
47
|
Pinheiro A, Faustino I, Silva MJ, Silva J, Sá R, Sousa M, Barros A, de Almeida IT, Rivera I. Human testis-specific PDHA2 gene: methylation status of a CpG island in the open reading frame correlates with transcriptional activity. Mol Genet Metab 2010; 99:425-30. [PMID: 20005141 DOI: 10.1016/j.ymgme.2009.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Revised: 11/11/2009] [Accepted: 11/11/2009] [Indexed: 11/26/2022]
Abstract
DNA methylation is an important epigenetic modification that has profound roles in gene expression and, in particular, is thought to be crucial for regulation of tissue-specific genes in animal cells. The pivotal E(1)alpha subunit of human pyruvate dehydrogenase complex, an essential and rate-limiting enzyme system in energy metabolism, is encoded by two distinct genes: PDHA1 gene, located on chromosome X is expressed in somatic tissues, whereas PDHA2 gene, located on chromosome 4, is exclusively expressed in spermatogenic cells. The objective of this study is to elucidate the role of DNA methylation as an epigenetic mechanism controlling the regulation of PDHA2 gene expression in human tissues, namely its repression in somatic tissues and its activation in testicular germ cells. Genomic DNA was isolated from human somatic tissues (circulating lymphocytes and gastric cells) and from testis, including isolated fractions of haploid and diploid germ cells. After primer design with appropriate software, it was performed the sodium bisulfite PCR sequencing of the PDHA2 promoter and coding regions. Total RNA of the same tissues was isolated, reverse transcribed and PDHA1and PDHA2 transcripts were amplified with specific primers and analysed by agarose gel electrophoresis. The analysis of the genomic sequence of the PDHA2 gene revealed the presence of 61 CpG sites whose distribution matches the criteria for the presence of two CpG islands. Sequence analysis of both CpG islands upon bisulfite treatment displayed several differences, either between islands or among tissues. In particular, the methylation pattern of one of the CpG islands revealed a perfect correlation with transcriptional activity of the PDHA2 gene either in testis or in somatic tissues. Surprisingly, it is the full demethylation of the CpG island located in the coding region that seems to play a crucial role upon PDHA2 gene transcription in testis.
Collapse
Affiliation(s)
- Ana Pinheiro
- Metabolism & Genetics Group, iMed, Faculty of Pharmacy, University of Lisbon, Portugal
| | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Walsh TK, Brisson JA, Robertson HM, Gordon K, Jaubert-Possamai S, Tagu D, Edwards OR. A functional DNA methylation system in the pea aphid, Acyrthosiphon pisum. INSECT MOLECULAR BIOLOGY 2010; 19 Suppl 2:215-28. [PMID: 20482652 DOI: 10.1111/j.1365-2583.2009.00974.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Methylation of cytosine is one of the main epigenetic mechanisms involved in controlling gene expression. Here we show that the pea aphid (Acyrthosiphon pisum) genome possesses homologues to all the DNA methyltransferases found in vertebrates, and that 0.69% (+/-0.25%) of all cytosines are methylated. Identified methylation sites are predominantly restricted to the coding sequence of genes at CpG sites. We identify twelve methylated genes, including genes that interact with juvenile hormone, a key endocrine signal in insects. Bioinformatic prediction using CpG ratios for all predicted genes suggest that a large proportion of genes are methylated within the pea aphid.
Collapse
Affiliation(s)
- T K Walsh
- CSIRO Entomology, Centre for Environment and Life Sciences, Floreat Park, WA, Australia.
| | | | | | | | | | | | | |
Collapse
|
49
|
Feng Q, Stern JE, Hawes SE, Lu H, Jiang M, Kiviat NB. DNA methylation changes in normal liver tissues and hepatocellular carcinoma with different viral infection. Exp Mol Pathol 2010; 88:287-92. [PMID: 20079733 DOI: 10.1016/j.yexmp.2010.01.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Accepted: 01/07/2010] [Indexed: 02/06/2023]
Abstract
Hepatocellular carcinoma (HCC) is known to be associated with both HBV and HCV. While epigenetic changes have been previously reported to be associated with hepatocellular carcinoma (HCC), whether the epigenetic profile of HBC associated HCC differs from that of HCV-associated HCC is unclear. We analyzed DNA methylation of ten genes (APC, CCND2, CDKN2A, GSTP1, HOXA9, RARB, RASSF1, RUNX, SFRP1, and TWIST1) using MethyLight assays on 65 archived liver tissue blocks. Three genes (APC, CCND2, and GSTP1) were frequently methylated in normal liver tissues. Five genes (APC, CDKN2A, HOXA9, RASSF1, and RUNX) were significantly more frequently methylated in malignant liver tissues than normal liver tissues. Among HCC cases, HOXA9, RASSF1 and SFRP1 were methylated more frequently in HBV-positive HCC cases, while CDKN2A were significantly more frequently methylated in HCV-positive HCC cases. Our data support the hypothesis that HCC resulting from different viral etiologies is associated with different epigenetic changes.
Collapse
Affiliation(s)
- Qinghua Feng
- Department of Pathology, School of Medicine, University of Washington, Seattle, Washington 98109, USA.
| | | | | | | | | | | |
Collapse
|
50
|
Gigek CO, Leal MF, Silva PNO, Lisboa LCF, Lima EM, Calcagno DQ, Assumpção PP, Burbano RR, Smith MDAC. hTERTmethylation and expression in gastric cancer. Biomarkers 2009; 14:630-6. [DOI: 10.3109/13547500903225912] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|