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Abstract
Epigenetic regulation is facilitated by a battery of proteins that act as 'writers' or 'erasers' to add or remove biochemical modifications to DNA and histone proteins. DNA modifications, histone modifications and long noncoding RNAs function interdependently through reciprocal crosstalk. This review will focus on DNA methylation and DNA methyltransferases with emphasis on how biological and biochemical factors such as histone modifications and noncoding RNAs might play a role in modulating DNA methylation. Other physiological and biochemical factors that can modify DNA methylation marks will also be discussed including chemical exposures and inflammation.
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Affiliation(s)
- Raymond Lo
- Genetics & Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
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102
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HPVbase--a knowledgebase of viral integrations, methylation patterns and microRNAs aberrant expression: As potential biomarkers for Human papillomaviruses mediated carcinomas. Sci Rep 2015. [PMID: 26205472 PMCID: PMC4513345 DOI: 10.1038/srep12522] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Human papillomaviruses (HPVs) are extremely associated with different carcinomas. Despite consequential accomplishments, there is still need to establish more promising biomarkers to discriminate cancerous progressions. Therefore, we have developed HPVbase (http://crdd.osdd.net/servers/hpvbase/), a comprehensive resource for three major efficacious cancer biomarkers i.e. integration and breakpoint events, HPVs methylation patterns and HPV mediated aberrant expression of distinct host microRNAs (miRNAs). It includes clinically important 1257 integrants and integration sites from different HPV types i.e. 16, 18, 31, 33 and 45 associated with distinct histological conditions. An inclusive HPV integrant and breakpoints browser was designed to provide easy browsing and straightforward analysis. Our study also provides 719 major quantitative HPV DNA methylation observations distributed in 5 distinct HPV genotypes from higher to lower in numbers namely HPV 16 (495), HPV 18 (113), HPV45 (66), HPV 31 (34) and HPV 33 (11). Additionally, we have curated and compiled clinically significant aberrant expression profile of 341 miRNAs including their target genes in distinct carcinomas, which can be utilized for miRNA therapeutics. A user-friendly web interface has been developed for easy data retrieval and analysis. We foresee that HPVbase an integrated and multi-comparative platform would facilitate reliable cancer diagnostics and prognosis.
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103
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Almamun M, Levinson BT, Gater ST, Schnabel RD, Arthur GL, Davis JW, Taylor KH. Genome-wide DNA methylation analysis in precursor B-cells. Epigenetics 2015; 9:1588-95. [PMID: 25484143 PMCID: PMC4622941 DOI: 10.4161/15592294.2014.983379] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
DNA methylation is responsible for regulating gene expression and cellular differentiation and for maintaining genomic stability during normal human development. Furthermore, it plays a significant role in the regulation of hematopoiesis. In order to elucidate the influence of DNA methylation during B-cell development, genome-wide DNA methylation status of pro-B, pre-BI, pre-BII, and naïve-B-cells isolated from human umbilical cord blood was determined using the methylated CpG island recovery assay followed by next generation sequencing. On average, 182–200 million sequences were generated for each precursor B-cell subset in 10 biological replicates. An overall decrease in methylation was observed during the transition from pro-B to pre-BI, whereas no differential methylation was observed in the pre-BI to pre-BII transition or in the pre-BII to naïve B-cell transition. Most of the methylated regions were located within intergenic and intronic regions not present in a CpG island context. Putative novel enhancers were identified in these regions that were differentially methylated between pro-B and pre-BI cells. The genome-wide methylation profiles are publically available and may be used to gain a better understanding of the involvement of atypical DNA methylation in the pathogenesis of malignancies associated with precursor B-cells.
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Key Words
- CG dinucleotide
- CLP, common lymphoid progenitor cells
- CpGI, CpG island
- DMRs, differentially methylated regions
- DNA methylation
- FDR, false discovery rate.
- H3K27ac, histone H3 lysine 27 acetylation
- H3K4me1, histone H3 lysine 4 monomethylation
- HCB, human umbilical cord blood
- HSCs, haematopoietic stem cells
- MBDs, methyl CpG binding domains
- MIRA-seq, methylated CpG island recovery assay (MIRA) followed by next generation sequencing
- MeCP2, methyl CpG binding protein 2
- Pre-B, precursor B-cell; CD
- Pro-B, progenitor B-cell
- ROIs, regions of interest
- TFs, transcription factors
- acute lymphoblastic leukemia; CpG
- cluster of differentiation; ALL
- enhancer
- next-generation sequencing
- precursor B-cell
- umbilical cord blood
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Affiliation(s)
- Md Almamun
- a Department of Pathology and Anatomical Sciences ; University of Missouri-Columbia ; Columbia , MO USA
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104
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Aschenbrenner D, Baumann F, Milles LF, Pippig DA, Gaub HE. C-5 Propynyl Modifications Enhance the Mechanical Stability of DNA. Chemphyschem 2015; 16:2085-90. [PMID: 25982589 DOI: 10.1002/cphc.201500193] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Indexed: 11/10/2022]
Abstract
Increased thermal or mechanical stability of DNA duplexes is desired for many applications in nanotechnology or -medicine where DNA is used as a programmable building block. Modifications of pyrimidine bases are known to enhance thermal stability and have the advantage of standard base-pairing and easy integration during chemical DNA synthesis. Through single-molecule force spectroscopy experiments with atomic force microscopy and the molecular force assay we investigated the effect of pyrimidines harboring C-5 propynyl modifications on the mechanical stability of double-stranded DNA. Utilizing these complementary techniques, we show that propynyl bases significantly increase the mechanical stability if the DNA is annealed at high temperature. In contrast, modified DNA complexes formed at room temperature and short incubation times display the same stability as non-modified DNA duplexes.
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Affiliation(s)
- Daniela Aschenbrenner
- Center for Nanoscience and Department of Physics, University of Munich, Amalienstrasse 54, 80799 München (Germany)
| | - Fabian Baumann
- Center for Nanoscience and Department of Physics, University of Munich, Amalienstrasse 54, 80799 München (Germany)
| | - Lukas F Milles
- Center for Nanoscience and Department of Physics, University of Munich, Amalienstrasse 54, 80799 München (Germany)
| | - Diana A Pippig
- Center for Nanoscience and Department of Physics, University of Munich, Amalienstrasse 54, 80799 München (Germany). .,Munich Center for Integrated Protein Science (CIPSM), Butenandtstr. 5-13, 81377 München (Germany).
| | - Hermann E Gaub
- Center for Nanoscience and Department of Physics, University of Munich, Amalienstrasse 54, 80799 München (Germany)
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105
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Keelawat S, Thorner PS, Shuangshoti S, Bychkov A, Kitkumthorn N, Rattanatanyong P, Boonyayothin W, Poumsuk U, Ruangvejvorachai P, Mutirangura A. Detection of global hypermethylation in well-differentiated thyroid neoplasms by immunohistochemical (5-methylcytidine) analysis. J Endocrinol Invest 2015; 38:725-32. [PMID: 25740063 DOI: 10.1007/s40618-015-0246-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 01/20/2015] [Indexed: 12/13/2022]
Abstract
PURPOSE While global hypomethylation of DNA has been found in several malignancies, studies on thyroid tumours have shown controversial results using different techniques. To help resolve this issue, we assessed methylation status using two different techniques in papillary thyroid carcinomas (PTC) and follicular adenomas (FA) and carcinomas (FTC), comparing adjacent non-neoplastic thyroid tissue. METHODS A series of 15 FA, 18 FTC and 17 PTC were assessed by: (1) measurement of methylation levels of long interspersed nuclear elements (LINE-1) using a combined bisulfite restriction analysis polymerase chain reaction protocol and (2) immunostaining with an anti-5-methylcytidine antibody that detects methylated DNA regardless of the DNA sequence. Immunostaining was scored by image analysis. RESULTS Methylation levels of LINE-1 in FA, FTC and PTC were not significantly different from adjacent normal tissue. There was no significant difference in methylation levels of LINE-1 between FA, FTC and PTC (p = 0.44). By immunohistochemical staining for methylation, the 5-methylcytidine score was significantly higher in tumours than in normal tissue counterparts, for FA (p < 0.001), FTC (p = 0.04) and PTC (p = 0.02). PTC showed the highest 5-methylcytidine expression amongst all tumours which was significantly different from FTC (p = 0.015), but not FA (p = 0.09). There was no correlation in methylation level between LINE-1 and 5-methylcytidine scores for each group and overall. CONCLUSIONS Well-differentiated thyroid neoplasms (FA, FTC and PTC) were not found by two independent methods to undergo global hypomethylation as part of an oncogenic sequence from normal tissue to carcinoma. Instead, hypermethylation was detected in all types of tumours, implying that this epigenetic event may contribute to oncogenic development of thyroid neoplasms (both benign and malignant).
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Affiliation(s)
- S Keelawat
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand.
| | - P S Thorner
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
- Division of Pathology, Hospital for Sick Children, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - S Shuangshoti
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
| | - A Bychkov
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
| | - N Kitkumthorn
- Department of Oral and Maxillofacial Pathology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand
- Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - P Rattanatanyong
- Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - W Boonyayothin
- Department of Pathology, Chonburi Hospital, 69 Moo 2, Tambon Baan Seaun, Ampur Mueung, Chonburi, Thailand
| | - U Poumsuk
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
| | - P Ruangvejvorachai
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
| | - A Mutirangura
- Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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106
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Bellacosa A, Drohat AC. Role of base excision repair in maintaining the genetic and epigenetic integrity of CpG sites. DNA Repair (Amst) 2015; 32:33-42. [PMID: 26021671 DOI: 10.1016/j.dnarep.2015.04.011] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cytosine methylation at CpG dinucleotides is a central component of epigenetic regulation in vertebrates, and the base excision repair (BER) pathway is important for maintaining both the genetic stability and the methylation status of CpG sites. This perspective focuses on two enzymes that are of particular importance for the genetic and epigenetic integrity of CpG sites, methyl binding domain 4 (MBD4) and thymine DNA glycosylase (TDG). We discuss their capacity for countering C to T mutations at CpG sites, by initiating base excision repair of G · T mismatches generated by deamination of 5-methylcytosine (5mC). We also consider their role in active DNA demethylation, including pathways that are initiated by oxidation and/or deamination of 5mC.
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Affiliation(s)
- Alfonso Bellacosa
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, United States.
| | - Alexander C Drohat
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St., Baltimore, MD 21201, United States.
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107
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Yi JM, Kim TO. Epigenetic alterations in inflammatory bowel disease and cancer. Intest Res 2015; 13:112-21. [PMID: 25931995 PMCID: PMC4414752 DOI: 10.5217/ir.2015.13.2.112] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 01/14/2015] [Accepted: 01/14/2015] [Indexed: 12/15/2022] Open
Abstract
Overwhelming evidences supports the idea that inflammatory bowel disease (IBD) is caused by a complex interplay between genetic alterations of multiple genes and an aberrant interaction with environmental factors. There is growing evidence that epigenetic factors can play a significant part in the pathogenesis of IBD. Significant effort has been invested in uncovering genetic and epigenetic factors, which may increase the risk of IBD, but progress has been slow, and few IBD-specific factors have been detected so far. It has been known for decades that DNA methylation is the most well studied epigenetic modification, and analysis of DNA methylation is leading to a new generation of cancer biomarkers. Therefore, in this review, we summarize the role of DNA methylation alteration in IBD pathogenesis, and discuss specific genes or genetic loci using recent molecular technology advances. Here, we suggest that DNA methylation should be studied in depth to understand the molecular pathways of IBD pathogenesis, and discuss epigenetic studies of IBD that may have a significant impact on the field of IBD research.
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Affiliation(s)
- Joo Mi Yi
- Research Institute, Dongnam Institute of Radiological & Medical Sciences (DIRAMS), Busan, Korea
| | - Tae Oh Kim
- Department of Internal Medicine, Haeundae Paik Hospital, Inje University College of Medicine, Busan, Korea
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108
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Lillycrop KA, Costello PM, Teh AL, Murray RJ, Clarke-Harris R, Barton SJ, Garratt ES, Ngo S, Sheppard AM, Wong J, Dogra S, Burdge GC, Cooper C, Inskip HM, Gale CR, Gluckman PD, Harvey NC, Chong YS, Yap F, Meaney MJ, Rifkin-Graboi A, Holbrook JD, Godfrey KM. Association between perinatal methylation of the neuronal differentiation regulator HES1 and later childhood neurocognitive function and behaviour. Int J Epidemiol 2015; 44:1263-76. [PMID: 25906782 PMCID: PMC4588869 DOI: 10.1093/ije/dyv052] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Background Early life environments induce long-term changes in neurocognitive development and behaviour. In animal models, early environmental cues affect neuropsychological phenotypes via epigenetic processes but, as yet, there is little direct evidence for such mechanisms in humans. Method We examined the relation between DNA methylation at birth and child neuropsychological outcomes in two culturally diverse populations using a genome-wide methylation analysis and validation by pyrosequencing. Results Within the UK Southampton Women’s Survey (SWS) we first identified 41 differentially methylated regions of interest (DMROI) at birth associated with child’s full-scale IQ at age 4 years. Associations between HES1 DMROI methylation and later cognitive function were confirmed by pyrosequencing in 175 SWS children. Consistent with these findings, higher HES1 methylation was associated with higher executive memory function in a second independent group of 200 SWS 7-year-olds. Finally, we examined a pathway for this relationship within a Singaporean cohort (n = 108). Here, HES1 DMROI methylation predicted differences in early infant behaviour, known to be associated with academic success. In vitro, methylation of HES1 inhibited ETS transcription factor binding, suggesting a functional role of this site. Conclusions Thus, our findings suggest that perinatal epigenetic processes mark later neurocognitive function and behaviour, providing support for a role of epigenetic processes in mediating the long-term consequences of early life environment on cognitive development.
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Affiliation(s)
- Karen A Lillycrop
- Centre for Biological Sciences, and NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK,
| | - Paula M Costello
- Academic Unit of Human Development and Health, University of Southampton, Southampton, UK
| | - Ai Ling Teh
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore
| | - Robert J Murray
- Academic Unit of Human Development and Health, University of Southampton, Southampton, UK
| | - Rebecca Clarke-Harris
- Academic Unit of Human Development and Health, University of Southampton, Southampton, UK
| | - Sheila J Barton
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - Emma S Garratt
- Academic Unit of Human Development and Health, University of Southampton, Southampton, UK
| | - Sherry Ngo
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Allan M Sheppard
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Johnny Wong
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore
| | - Shaillay Dogra
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore
| | - Graham C Burdge
- Academic Unit of Human Development and Health, University of Southampton, Southampton, UK
| | - Cyrus Cooper
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK, NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK, NIHR Musculoskeletal Biomedical Research Unit, University of Oxford, Oxford, UK
| | - Hazel M Inskip
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - Catharine R Gale
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK, Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Peter D Gluckman
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore, Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Nicholas C Harvey
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - Yap-Seng Chong
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore, Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Fabian Yap
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Duke NUS Graduate School of Medicine, National University of Singapore, Singapore, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore and
| | - Michael J Meaney
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore, Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montréal, Canada
| | - Anne Rifkin-Graboi
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore
| | - Joanna D Holbrook
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore
| | | | - Keith M Godfrey
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK, NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
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109
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Song Q, Chen ZJ. Epigenetic and developmental regulation in plant polyploids. CURRENT OPINION IN PLANT BIOLOGY 2015; 24:101-9. [PMID: 25765928 PMCID: PMC4395545 DOI: 10.1016/j.pbi.2015.02.007] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 02/18/2015] [Accepted: 02/18/2015] [Indexed: 05/18/2023]
Abstract
Polyploidy or whole-genome duplication occurs in some animals and many flowering plants, including many important crops such as wheat, cotton and oilseed rape. The prevalence of polyploidy in the plant kingdom suggests it as an important evolutionary feature for plant speciation and crop domestication. Studies of natural and synthetic polyploids have revealed rapid and dynamic changes in genomic structure and gene expression after polyploid formation. Growing evidence suggests that epigenetic modifications can alter homoeologous gene expression and reprogram gene expression networks, which allows polyploids to establish new cytotypes, grow vigorously and promote adaptation in local environments. Sequence and gene expression changes in polyploids have been well documented and reviewed elsewhere. This review is focused on developmental regulation and epigenetic changes including DNA methylation and histone modifications in polyploids.
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Affiliation(s)
- Qingxin Song
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
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110
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Tarnowski M, Tkacz M, Czerewaty M, Poniewierska-Baran A, Grymuła K, Ratajczak MZ. 5‑Azacytidine inhibits human rhabdomyosarcoma cell growth by downregulating insulin‑like growth factor 2 expression and reactivating the H19 gene product miR‑675, which negatively affects insulin‑like growth factors and insulin signaling. Int J Oncol 2015; 46:2241-50. [PMID: 25707431 DOI: 10.3892/ijo.2015.2906] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 12/29/2014] [Indexed: 11/05/2022] Open
Abstract
Insulin-like growth factor 2 (IGF2) and 1 (IGF1) and insulin (INS) promote proliferation of rhabdomyosarcoma (RMS) cells by interacting with the insulin-like growth factor 1 receptor (IGF1R) and the insulin receptor (INSR). Loss of imprinting (LOI) by DNA hypermethylation at the differentially methylated region (DMR) for the IGF2‑H19 locus is commonly observed in RMS cells and results in an increase in the expression of proliferation-promoting IGF2 and downregulation of proliferation-inhibiting non-coding H19 miRNAs. One of these miRNAs, miR‑675, has been reported in murine cells to be a negative regulator of IGF1R expression. To better address the role of IGF2 and 1, as well as INS signaling in the pathogenesis of RMS and the involvement of LOI at the IGF2‑H19 locus, we employed the DNA demethylating agent 5‑azacytidine (AzaC). We observed that AzaC‑mediated demethylation of the DMR at the IGF2‑H19 locus resulted in downregulation of IGF2 and an increase in the expression of H19. This epigenetic change resulted in a decrease in RMS proliferation due to downregulation of IGF2 and, IGF1R expression in an miR‑675‑dependent manner. Interestingly, we observed that miR‑675 not only inhibited the expression of IGF1R in a similar manner in human and murine cells, but we also observed its negative effect on the expression of the INSR. These results confirm the crucial role of LOI at the IGF2‑H19 DMR in the pathogenesis of RMS and are relevant to the development of new treatment strategies.
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Affiliation(s)
- Maciej Tarnowski
- Department of Physiology Pomeranian Medical University, Szczecin, Poland
| | - Marta Tkacz
- Department of Physiology Pomeranian Medical University, Szczecin, Poland
| | - Michał Czerewaty
- Department of Physiology Pomeranian Medical University, Szczecin, Poland
| | | | - Katarzyna Grymuła
- Department of Physiology Pomeranian Medical University, Szczecin, Poland
| | - Mariusz Z Ratajczak
- Stem Cell Biology Program at the James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
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111
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Abstract
It is well established that genotype plays an important role in the ageing process. However, recent studies have suggested that epigenetic mechanisms may also influence the onset of ageing-associated diseases and longevity. Epigenetics is defined as processes that induce heritable changes in gene expression without a change in the DNA nucleotide sequence. The major epigenetic mechanisms are DNA methylation, histone modification and non-coding RNA. Such processes are involved in the regulation of tissue-specific gene expression, cell differentiation and genomic imprinting. However, epigenetic dysregulation is frequently seen with ageing. Relatively little is known about the factors that initiate such changes. However, there is emerging evidence that the early life environment, in particular nutrition, in early life can induce long-term changes in DNA methylation resulting in an altered susceptibility to a range of ageing-associated diseases. In this review, we will focus on the changes in DNA methylation that occur during ageing; their role in the ageing process and how early life nutrition can modulate DNA methylation and influence longevity. Understanding the mechanisms by which diet in early life can influence the epigenome will be crucial for the development of preventative and intervention strategies to increase well-being in later life.
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112
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Liu Y, Zheng W, Zhang W, Chen N, Liu Y, Chen L, Zhou X, Chen X, Zheng H, Li X. Photoaffinity labeling of transcription factors by DNA-templated crosslinking. Chem Sci 2015; 6:745-751. [PMID: 28706637 PMCID: PMC5494549 DOI: 10.1039/c4sc01953a] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 09/30/2014] [Indexed: 12/24/2022] Open
Abstract
Characterization of transcription factor-DNA interaction is of high importance in elucidating the molecular mechanisms of gene transcriptions. DNA-based affinity probes were developed to capture and identify transcription factors by covalent crosslinking; however, the requirement of a crosslinker on the affinity probe remains a disadvantage, as the crosslinker itself often interferes with the protein-DNA interactions. We report a dual-probe method able to capture DNA-binding transcription factors with unmodified protein-binding sites in scenarios where conventional probes have failed. We have also shown the method's converse application in selecting specific transcription factor-binding DNA sequences from a probe library and its extension to studying proteins recognizing epigenetic marks. This study may provide a new tool for exploring DNA-binding proteins in biology.
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Affiliation(s)
- Ying Liu
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Wenlu Zheng
- Key Laboratory of Chemical Genomics , School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen , China 518055
| | - Wan Zhang
- Key Laboratory of Chemical Genomics , School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen , China 518055
| | - Nan Chen
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Yang Liu
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Li Chen
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Xiaozhou Zhou
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Xingshuo Chen
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Haifeng Zheng
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Xiaoyu Li
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
- Key Laboratory of Chemical Genomics , School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen , China 518055
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113
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Abstract
Cytosine methylation in DNA constitutes an important epigenetic layer of transcriptional and regulatory control in many eukaryotes. Profiling DNA methylation across the genome is critical to understanding the influence of epigenetics in normal biology and disease, such as cancer. Genome-wide analyses such as arrays and next-generation sequencing (NGS) technologies have been used to assess large fractions of the methylome at a single-base-pair resolution. However, the range of DNA methylation profiling techniques can make selecting the appropriate protocol a challenge. This chapter discusses the advantages and disadvantages of various methylome detection approaches to assess which is appropriate for the question at hand. Here, we focus on four prominent genome-wide approaches: whole-genome bisulfite sequencing (WGBS); methyl-binding domain capture sequencing (MBDCap-Seq); reduced-representation-bisulfite-sequencing (RRBS); and Infinium Methylation450 BeadChips (450 K, Illumina). We discuss some of the requirements, merits, and challenges that should be considered when choosing a methylome technology to ensure that it will be informative. In addition, we show how genome-wide methylation detection arrays and high-throughput sequencing have provided immense insight into ovarian cancer-specific methylation signatures that may serve as diagnostic biomarkers or predict patient response to epigenetic therapy.
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Gangisetty O, Bekdash R, Maglakelidze G, Sarkar DK. Fetal alcohol exposure alters proopiomelanocortin gene expression and hypothalamic-pituitary-adrenal axis function via increasing MeCP2 expression in the hypothalamus. PLoS One 2014; 9:e113228. [PMID: 25409090 PMCID: PMC4237387 DOI: 10.1371/journal.pone.0113228] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 10/21/2014] [Indexed: 11/19/2022] Open
Abstract
Proopiomelanocortin (POMC) is a precursor gene of the neuropeptide β-endorphin in the hypothalamus and is known to regulate various physiological functions including stress response. Several recent reports showed that fetal alcohol exposure programs the hypothalamus to produce lower levels of POMC gene transcripts and to elevate the hypothalamic-pituitary-adrenal (HPA) axis response to stressful stimuli. We investigated the role of methyl CpG binding protein (MeCP2) in the effects of prenatal ethanol on POMC gene expression and hypothalamic-pituitary-adrenal (HPA) axis function. Pregnant Sprague Dawley rats were fed between GD 7 and 21 with a liquid diet containing 6.7% alcohol, pair-fed with isocaloric liquid diet, or fed ad libitum with rat chow, and their male offsprings were used at 60 days after birth in this study. Fetal alcohol exposure reduced the level of POMC mRNA, but increased the level of DNA methylation of this gene in the arcuate nucleus (ARC) of the hypothalamus where the POMC neuronal cell bodies are located. Fetal alcohol exposed rats showed a significant increase in MeCP2 protein levels in POMC cells, MeCP2 gene transcript levels as well as increased MeCP2 protein binding on the POMC promoter in the arcuate nucleus. Lentiviral delivery of MeCP2 shRNA into the third ventricle efficiently reduced MeCP2 expression and prevented the effect of prenatal ethanol on POMC gene expression in the arcuate nucleus. MeCP2-shRNA treatment also normalized the prenatal ethanol-induced increase in corticotropin releasing hormone (CRH) gene expression in the hypothalamus and elevated plasma adrenocorticotrophic hormone (ACTH) and corticosterone hormone responses to lipopolysaccharide (LPS) challenge. These results suggest that fetal alcohol programming of POMC gene may involve recruitment of MeCP2 on to the methylated promoter of the POMC gene to suppress POMC transcript levels and contribute to HPA axis dysregulation.
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Affiliation(s)
- Omkaram Gangisetty
- Endocrine Program, Department of Animal Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Rola Bekdash
- Endocrine Program, Department of Animal Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
| | - George Maglakelidze
- Endocrine Program, Department of Animal Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Dipak K. Sarkar
- Endocrine Program, Department of Animal Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
- * E-mail:
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Maroni L, Pierantonelli I, Banales JM, Benedetti A, Marzioni M. The significance of genetics for cholangiocarcinoma development. ANNALS OF TRANSLATIONAL MEDICINE 2014; 1:28. [PMID: 25332972 DOI: 10.3978/j.issn.2305-5839.2012.10.04] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 10/15/2012] [Indexed: 12/15/2022]
Abstract
Cholangiocarcinoma (CCA) is a rare malignancy of the liver, arising from bile ducts. The incidence is increasing worldwide, but the prognosis has remained dismal and virtually unchanged in the past 30 years. Although several risk factors have been associated with the development of this cancer, none of them are normally identified in most patients. Diagnosis in advanced stages of the disease and limited therapeutic options contribute to poor survival rates. The recent analysis of genetic and epigenetic alterations occurring in CCA has shed new light in the understanding of the molecular mechanisms leading to the malignant transformation of biliary cells. Further studies in this direction may foster new diagnostic, prognostic and therapeutic approaches. This review provides a global overview of recent advances in CCA and describes the most important genetic mutations and epigenetic alterations so far reported in CCA.
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Affiliation(s)
- Luca Maroni
- 1 Department of Gastroenterology, Università Politecnica delle Marche, Ancona, Italy ; 2 Department of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands ; 3 Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria ; 4 Division of Hepatology and Gastroenterology, Biodonostia Research Institute (Donostia University Hospital), CIBERehd, University of Basque Country, San Sebastián, Spain - IKERBASQUE (Basque Foundation of Science), and "Asociación Española Contra el Cáncer, (AECC)"
| | - Irene Pierantonelli
- 1 Department of Gastroenterology, Università Politecnica delle Marche, Ancona, Italy ; 2 Department of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands ; 3 Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria ; 4 Division of Hepatology and Gastroenterology, Biodonostia Research Institute (Donostia University Hospital), CIBERehd, University of Basque Country, San Sebastián, Spain - IKERBASQUE (Basque Foundation of Science), and "Asociación Española Contra el Cáncer, (AECC)"
| | - Jesus M Banales
- 1 Department of Gastroenterology, Università Politecnica delle Marche, Ancona, Italy ; 2 Department of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands ; 3 Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria ; 4 Division of Hepatology and Gastroenterology, Biodonostia Research Institute (Donostia University Hospital), CIBERehd, University of Basque Country, San Sebastián, Spain - IKERBASQUE (Basque Foundation of Science), and "Asociación Española Contra el Cáncer, (AECC)"
| | - Antonio Benedetti
- 1 Department of Gastroenterology, Università Politecnica delle Marche, Ancona, Italy ; 2 Department of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands ; 3 Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria ; 4 Division of Hepatology and Gastroenterology, Biodonostia Research Institute (Donostia University Hospital), CIBERehd, University of Basque Country, San Sebastián, Spain - IKERBASQUE (Basque Foundation of Science), and "Asociación Española Contra el Cáncer, (AECC)"
| | - Marco Marzioni
- 1 Department of Gastroenterology, Università Politecnica delle Marche, Ancona, Italy ; 2 Department of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands ; 3 Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria ; 4 Division of Hepatology and Gastroenterology, Biodonostia Research Institute (Donostia University Hospital), CIBERehd, University of Basque Country, San Sebastián, Spain - IKERBASQUE (Basque Foundation of Science), and "Asociación Española Contra el Cáncer, (AECC)"
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116
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Rao MK, Matsumoto Y, Richardson ME, Panneerdoss S, Bhardwaj A, Ward JM, Shanker S, Bettegowda A, Wilkinson MF. Hormone-induced and DNA demethylation-induced relief of a tissue-specific and developmentally regulated block in transcriptional elongation. J Biol Chem 2014; 289:35087-101. [PMID: 25331959 DOI: 10.1074/jbc.m114.615435] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Genome-wide studies have revealed that genes commonly have a high density of RNA polymerase II just downstream of the transcription start site. This has raised the possibility that genes are commonly regulated by transcriptional elongation, but this remains largely untested in vivo, particularly in vertebrates. Here, we show that the proximal promoter from the Rhox5 homeobox gene recruits polymerase II and begins elongating in all tissues and cell lines that we tested, but it only completes elongation in a tissue-specific and developmentally regulated manner. Relief of the elongation block is associated with recruitment of the elongation factor P-TEFb, the co-activator GRIP1, the chromatin remodeling factor BRG1, and specific histone modifications. We provide evidence that two mechanisms relieve the elongation block at the proximal promoter: demethylation and recruitment of androgen receptor. Together, our findings support a model in which promoter proximal pausing helps confer tissue-specific and developmental gene expression through a mechanism regulated by DNA demethylation-dependent nuclear hormone receptor recruitment.
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Affiliation(s)
- Manjeet K Rao
- From the Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, the Greehey Children's Cancer Research Institute, Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio, Texas 78229
| | - Yuiko Matsumoto
- From the Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030
| | - Marcy E Richardson
- the Department of Reproductive Medicine, University of California at San Diego, La Jolla, California 92037, the Institute of Genomic Medicine, University of California at San Diego, La Jolla, California 92093, and
| | - Subbarayalu Panneerdoss
- the Greehey Children's Cancer Research Institute, Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio, Texas 78229
| | - Anjana Bhardwaj
- From the Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030
| | - Jacqueline M Ward
- the Department of Reproductive Medicine, University of California at San Diego, La Jolla, California 92037, the Institute of Genomic Medicine, University of California at San Diego, La Jolla, California 92093, and
| | - Sreenath Shanker
- From the Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030
| | - Anilkumar Bettegowda
- From the Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, the Department of Reproductive Medicine, University of California at San Diego, La Jolla, California 92037, the Institute of Genomic Medicine, University of California at San Diego, La Jolla, California 92093, and
| | - Miles F Wilkinson
- From the Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, the Department of Reproductive Medicine, University of California at San Diego, La Jolla, California 92037, the Institute of Genomic Medicine, University of California at San Diego, La Jolla, California 92093, and
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117
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Miyata K, Miyata T, Nakabayashi K, Okamura K, Naito M, Kawai T, Takada S, Kato K, Miyamoto S, Hata K, Asahara H. DNA methylation analysis of human myoblasts during in vitro myogenic differentiation: de novo methylation of promoters of muscle-related genes and its involvement in transcriptional down-regulation. Hum Mol Genet 2014; 24:410-23. [PMID: 25190712 DOI: 10.1093/hmg/ddu457] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Although DNA methylation is considered to play an important role during myogenic differentiation, chronological alterations in DNA methylation and gene expression patterns in this process have been poorly understood. Using the Infinium HumanMethylation450 BeadChip array, we obtained a chronological profile of the genome-wide DNA methylation status in a human myoblast differentiation model, where myoblasts were cultured in low-serum medium to stimulate myogenic differentiation. As the differentiation of the myoblasts proceeded, their global DNA methylation level increased and their methylation patterns became more distinct from those of mesenchymal stem cells. Gene ontology analysis revealed that genes whose promoter region was hypermethylated upon myoblast differentiation were highly significantly enriched with muscle-related terms such as 'muscle contraction' and 'muscle system process'. Sequence motif analysis identified 8-bp motifs somewhat similar to the binding motifs of ID4 and ZNF238 to be most significantly enriched in hypermethylated promoter regions. ID4 and ZNF238 have been shown to be critical transcriptional regulators of muscle-related genes during myogenic differentiation. An integrated analysis of DNA methylation and gene expression profiles revealed that de novo DNA methylation of non-CpG island (CGI) promoters was more often associated with transcriptional down-regulation than that of CGI promoters. These results strongly suggest the existence of an epigenetic mechanism in which DNA methylation modulates the functions of key transcriptional factors to coordinately regulate muscle-related genes during myogenic differentiation.
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Affiliation(s)
- Kohei Miyata
- Department of Systems BioMedicine and Department of Obstetrics and Gynecology, Faculty of Medicine, Fukuoka University, Fukuoka 814-0180, Japan
| | - Tomoko Miyata
- Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Kazuhiko Nakabayashi
- Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | | | - Masashi Naito
- Department of Systems BioMedicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan and
| | - Tomoko Kawai
- Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | | | - Kiyoko Kato
- Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Shingo Miyamoto
- Department of Obstetrics and Gynecology, Faculty of Medicine, Fukuoka University, Fukuoka 814-0180, Japan
| | - Kenichiro Hata
- Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Hiroshi Asahara
- Department of Systems BioMedicine and Department of Systems BioMedicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan and Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
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118
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Demethylation within the proximal promoter region of human estrogen receptor alpha gene correlates with its enhanced expression: Implications for female bias in lupus. Mol Immunol 2014; 61:28-37. [DOI: 10.1016/j.molimm.2014.05.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Revised: 04/28/2014] [Accepted: 05/02/2014] [Indexed: 11/19/2022]
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119
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Siegel EM, Eschrich S, Winter K, Riggs B, Berglund A, Ajidahun A, Simko J, Moughan J, Ajani J, Magliocco A, Elahi A, Hoffe S, Shibata D. Epigenomic characterization of locally advanced anal cancer: a radiation therapy oncology group 98-11 specimen study. Dis Colon Rectum 2014; 57:941-57. [PMID: 25003289 PMCID: PMC4100249 DOI: 10.1097/dcr.0000000000000160] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND The Radiation Therapy Oncology Group 98-11 clinical trial demonstrated the superiority of standard 5-fluorouracil/mitomycin-C over 5-fluorouracil/cisplatin in combination with radiation in the treatment of anal squamous cell cancer. Tumor size (>5 cm) and lymph node metastases are associated with disease progression. There may be key molecular differences (eg, DNA methylation changes) in tumors at high risk for progression. OBJECTIVE The objectives of this study were to determine whether there are differences in DNA methylation at individual CpG sites and within genes among locally advanced anal cancers, with large tumor size and/or nodal involvement, compared with those that are less advanced. DESIGN This was a case-case study among 121 patients defined as high risk (tumor size >5 cm and/or nodal involvement; n = 59) or low risk (≤5 cm, node negative; n = 62) within the mitomycin-C arm of the Radiation Therapy Oncology Group 98-11 trial. DNA methylation was measured using the Illumina HumanMethylation450 Array. SETTINGS The study was conducted in a tertiary care cancer center in collaboration with a national clinical trials cooperative group. PATIENTS The patients consisted of 74 women and 47 men with a median age of 54 years (range, 25-79 years). MAIN OUTCOME MEASURES DNA methylation differences at individual CpG sites and within genes between low- and high-risk patients were compared using the Mann-Whitney test (p < 0.001). RESULTS A total of 16 CpG loci were differentially methylated (14 increased and 2 decreased) in high- versus low-risk cases. Genes harboring differentially methylated CpG sites included known tumor suppressor genes and novel targets. LIMITATIONS This study only included patients in the mitomycin-C arm with tumor tissue; however, this sample was representative of the trial. CONCLUSIONS This is the first study to apply genome-wide methylation analysis to anal cancer. Biologically relevant differences in methylated targets were found to discriminate locally advanced from early anal cancer. Epigenetic events likely play a significant role in the progression of anal cancer and may serve as potential biomarkers.
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Affiliation(s)
- Erin M Siegel
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL
| | - Steven Eschrich
- Department of Biomedical Informatics, Moffitt Cancer Center, Tampa, FL
| | - Kathryn Winter
- Department of Statistics, Radiation Therapy Oncology Group, Philadelphia, PA and San Francisco, CA
| | - Bridget Riggs
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL
| | - Anders Berglund
- Department of Biomedical Informatics, Moffitt Cancer Center, Tampa, FL
| | - Abidemi Ajidahun
- Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, FL
| | - Jeff Simko
- Department of Biospecimen Resource, Radiation Therapy Oncology Group, Philadelphia, PA and San Francisco, CA
| | - Jennifer Moughan
- Department of Statistics, Radiation Therapy Oncology Group, Philadelphia, PA and San Francisco, CA
| | - Jaffer Ajani
- Department of Medical Oncology, MD Anderson Cancer Center, Houston, TX
| | | | - Abul Elahi
- Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, FL
| | - Sarah Hoffe
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, FL
| | - David Shibata
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL,Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, FL
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120
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Anwar SL, Lehmann U. DNA methylation, microRNAs, and their crosstalk as potential biomarkers in hepatocellular carcinoma. World J Gastroenterol 2014; 20:7894-7913. [PMID: 24976726 PMCID: PMC4069317 DOI: 10.3748/wjg.v20.i24.7894] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 01/24/2014] [Accepted: 03/06/2014] [Indexed: 02/06/2023] Open
Abstract
Epigenetic alterations have been identified as a major characteristic in human cancers. Advances in the field of epigenetics have contributed significantly in refining our knowledge of molecular mechanisms underlying malignant transformation. DNA methylation and microRNA expression are epigenetic mechanisms that are widely altered in human cancers including hepatocellular carcinoma (HCC), the third leading cause of cancer related mortality worldwide. Both DNA methylation and microRNA expression patterns are regulated in developmental stage specific-, cell type specific- and tissue-specific manner. The aberrations are inferred in the maintenance of cancer stem cells and in clonal cell evolution during carcinogenesis. The availability of genome-wide technologies for DNA methylation and microRNA profiling has revolutionized the field of epigenetics and led to the discovery of a number of epigenetically silenced microRNAs in cancerous cells and primary tissues. Dysregulation of these microRNAs affects several key signalling pathways in hepatocarcinogenesis suggesting that modulation of DNA methylation and/or microRNA expression can serve as new therapeutic targets for HCC. Accumulative evidence shows that aberrant DNA methylation of certain microRNA genes is an event specifically found in HCC which correlates with unfavorable outcomes. Therefore, it can potentially serve as a biomarker for detection as well as for prognosis, monitoring and predicting therapeutic responses in HCC.
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121
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Massah S, Hollebakken R, Labrecque MP, Kolybaba AM, Beischlag TV, Prefontaine GG. Epigenetic characterization of the growth hormone gene identifies SmcHD1 as a regulator of autosomal gene clusters. PLoS One 2014; 9:e97535. [PMID: 24818964 PMCID: PMC4018343 DOI: 10.1371/journal.pone.0097535] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 04/21/2014] [Indexed: 12/31/2022] Open
Abstract
Regulatory elements for the mouse growth hormone (GH) gene are located distally in a putative locus control region (LCR) in addition to key elements in the promoter proximal region. The role of promoter DNA methylation for GH gene regulation is not well understood. Pit-1 is a POU transcription factor required for normal pituitary development and obligatory for GH gene expression. In mammals, Pit-1 mutations eliminate GH production resulting in a dwarf phenotype. In this study, dwarf mice illustrated that Pit-1 function was obligatory for GH promoter hypomethylation. By monitoring promoter methylation levels during developmental GH expression we found that the GH promoter became hypomethylated coincident with gene expression. We identified a promoter differentially methylated region (DMR) that was used to characterize a methylation-dependent DNA binding activity. Upon DNA affinity purification using the DMR and nuclear extracts, we identified structural maintenance of chromosomes hinge domain containing -1 (SmcHD1). To better understand the role of SmcHD1 in genome-wide gene expression, we performed microarray analysis and compared changes in gene expression upon reduced levels of SmcHD1 in human cells. Knock-down of SmcHD1 in human embryonic kidney (HEK293) cells revealed a disproportionate number of up-regulated genes were located on the X-chromosome, but also suggested regulation of genes on non-sex chromosomes. Among those, we identified several genes located in the protocadherin β cluster. In addition, we found that imprinted genes in the H19/Igf2 cluster associated with Beckwith-Wiedemann and Silver-Russell syndromes (BWS & SRS) were dysregulated. For the first time using human cells, we showed that SmcHD1 is an important regulator of imprinted and clustered genes.
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Affiliation(s)
- Shabnam Massah
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Robert Hollebakken
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Mark P. Labrecque
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Addie M. Kolybaba
- Faculty of Biology, Ludwig Maximilians University Munich, Martinsried, Germany
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Oliveira MVMD, Fraga CADC, Barros LO, Pereira CS, Santos SHS, Basile JR, Gomez RS, Guimarães ALS, De-Paula AMB. High expression of S100A4 and endoglin is associated with metastatic disease in head and neck squamous cell carcinoma. Clin Exp Metastasis 2014; 31:639-49. [PMID: 24798676 DOI: 10.1007/s10585-014-9655-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 04/20/2014] [Indexed: 01/22/2023]
Abstract
The presence of cervical metastasis is responsible for high morbidity and mortality rates in individuals with head and neck squamous cell carcinoma (HNSCC). S100A4, a pleiotropic EF-hand calcium-binding protein, is expressed in various normal and cancer cell types. During cancer progression, molecular disturbances in S100A4 can modulate the activity and expression of pre-metastatic and metastatic genes. In this study, we investigated the association between S100A4 methylation status and protein expression as well as the expression of the S100A4 related-proteins annexin A2 (ANXA2), matrix metallopeptidase-9, and endoglin, for metastasis and other clinicopathological parameters in HNSCC. Formalin-fixed, paraffin-embedded blocks of metastatic and non-metastatic HNSCC and matched cervical lymph node (LN) samples (metastatic LN = mLN, non-metastatic = nmLN, and control LN (lymphadenitis) = cLN) were submitted for methylation specific-polymerase chain reaction and immunohistochemistry. Our results showed that S100A4 methylation status failed to demonstrate association with cervical metastasis and other clinicopathological factors related to HNSCC. HNSCC samples from patients that presented with metastatic disease showed high S100A4 and endoglin expression (p < 0.05). In conclusion, molecular disturbances in S100A4 and endoglin expression might regulate the formation of cervical metastasis in HNSCC.
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Affiliation(s)
- Marcos Vinícius Macedo de Oliveira
- Nucleus of Epidemiological and Molecular Research Catrumano. Health Research Laboratory. Health Science Post-graduate Programme, Universidade Estadual de Montes Claros, Montes Claros, MG, 39401-001, Brazil
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123
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Rivière G. Epigenetic features in the oyster Crassostrea gigas suggestive of functionally relevant promoter DNA methylation in invertebrates. Front Physiol 2014; 5:129. [PMID: 24778620 PMCID: PMC3985014 DOI: 10.3389/fphys.2014.00129] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 03/14/2014] [Indexed: 12/22/2022] Open
Abstract
DNA methylation is evolutionarily conserved. Vertebrates exhibit high, widespread DNA methylation whereas invertebrate genomes are less methylated, predominantly within gene bodies. DNA methylation in invertebrates is associated with transcription level, alternative splicing, and genome evolution, but functional outcomes of DNA methylation remain poorly described in lophotrochozoans. Recent genome-wide approaches improve understanding in distant taxa such as molluscs, where the phylogenetic position, and life traits of Crassostrea gigas make this bivalve an ideal model to study the physiological and evolutionary implications of DNA methylation. We review the literature about DNA methylation in invertebrates and focus on DNA methylation features in the oyster. Indeed, though our MeDIP-seq results confirm predominant intragenic methylation, the profiles depend on the oyster's developmental and reproductive stage. We discuss the perspective that oyster DNA methylation could be biased toward the 5'-end of some genes, depending on physiological status, suggesting important functional outcomes of putative promoter methylation from cell differentiation during early development to sustained adaptation of the species to the environment.
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Affiliation(s)
- Guillaume Rivière
- Institute for Fundamental and Applied Biology, Normandy UniversityCaen, France
- UMR BOREA ‘Biologie des Organismes et Ecosystèmes Aquatiques’ Université de Caen Basse-Normandie, MNHN, UPMC, CNRS-7208, IRD-207Caen, France
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124
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Sassa A, Çağlayan M, Dyrkheeva NS, Beard WA, Wilson SH. Base excision repair of tandem modifications in a methylated CpG dinucleotide. J Biol Chem 2014; 289:13996-4008. [PMID: 24695738 DOI: 10.1074/jbc.m114.557769] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cytosine methylation and demethylation in tracks of CpG dinucleotides is an epigenetic mechanism for control of gene expression. The initial step in the demethylation process can be deamination of 5-methylcytosine producing the TpG alteration and T:G mispair, and this step is followed by thymine DNA glycosylase (TDG) initiated base excision repair (BER). A further consideration is that guanine in the CpG dinucleotide may become oxidized to 7,8-dihydro-8-oxoguanine (8-oxoG), and this could affect the demethylation process involving TDG-initiated BER. However, little is known about the enzymology of BER of altered in-tandem CpG dinucleotides; e.g. Tp8-oxoG. Here, we investigated interactions between this altered dinucleotide and purified BER enzymes, the DNA glycosylases TDG and 8-oxoG DNA glycosylase 1 (OGG1), apurinic/apyrimidinic (AP) endonuclease 1, DNA polymerase β, and DNA ligases. The overall TDG-initiated BER of the Tp8-oxoG dinucleotide is significantly reduced. Specifically, TDG and DNA ligase activities are reduced by a 3'-flanking 8-oxoG. In contrast, the OGG1-initiated BER pathway is blocked due to the 5'-flanking T:G mispair; this reduces OGG1, AP endonuclease 1, and DNA polymerase β activities. Furthermore, in TDG-initiated BER, TDG remains bound to its product AP site blocking OGG1 access to the adjacent 8-oxoG. These results reveal BER enzyme specificities enabling suppression of OGG1-initiated BER and coordination of TDG-initiated BER at this tandem alteration in the CpG dinucleotide.
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Affiliation(s)
- Akira Sassa
- From the Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709 and
| | - Melike Çağlayan
- From the Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709 and
| | - Nadezhda S Dyrkheeva
- From the Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709 and Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, 630090 Novosibirsk, Russia
| | - William A Beard
- From the Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709 and
| | - Samuel H Wilson
- From the Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709 and
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Epigenetic modification of FOXP3 in patients with chronic HIV infection. J Acquir Immune Defic Syndr 2014; 65:19-26. [PMID: 23846566 DOI: 10.1097/qai.0b013e3182a1bca4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
OBJECTIVES HIV-1 modulates host cell epigenetic machinery to control its own replication and induce immune suppression. HIV-1 infection leads to activation of T regulatory cell (T(reg)), but the mechanism underlying this immune modulation is unclear. T(reg) plays a prominent role in gut-mucosal immune tolerance by restraining excessive effector T-cell responses, a mechanism that is known to be disturbed in chronic HIV-1 infection. DNA methylation plays a major role in T(reg) lineage commitment and immune homeostasis, which may be regulated by HIV. To investigate the mechanisms of aberrant methylation of the T(reg) marker FOXP3 in HIV-1 infection, we evaluated the expression pattern of methylation-related enzymes and its correlation to FOXP3 methylation. METHODS FOXP3 promoter methylation in the colon mucosa and peripheral blood from HIV-infected patients and control subjects was measured using Pyrosequencing. Gene expression pattern of DNA methylation enzymes in the colon mucosa was investigated by Microarray and quantitative reverse transcriptase-polymerase chain reaction analysis in the same subjects. RESULTS FOXP3 promoter was significantly (P ≤ 0.0001) demethylated in HIV-infected patients compared with control subjects in both tissues. Expression of DNA methyltransferase 1 (DNAMT1), DNA methyltransferase 1-associated protein 1(DMAP1), methyltransferase-like 7B (METTL7B), and methyltransferase-like 10 (METTL10) were significantly down regulated in HIV-infected patients compared with controls and had a significant positive correlation to FOXP3 promoter methylation. CONCLUSIONS We present evidence suggesting that altered methylation pattern of FOXP3 and accordingly higher T(reg) frequency in gut mucosa of HIV-infected patients may be because of aberrant methylation processing in HIV.
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Molecular mechanisms of luteinization. Obstet Gynecol Sci 2014; 57:93-101. [PMID: 24678481 PMCID: PMC3965707 DOI: 10.5468/ogs.2014.57.2.93] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/29/2014] [Accepted: 02/04/2014] [Indexed: 11/24/2022] Open
Abstract
Dynamic changes in steroidogenesis occur in ovarian granulosa cells during ovulation after the LH surge. The ovulatory LH surge induces rapid up-regulation of steroidogenic acute regulatory (StAR) protein and rapid down-regulation of aromatase (Cyp19a1) in granulosa cells undergoing luteinization during ovulation. These rapid changes in StAR and Cyp19a1 gene expression after the LH surge efficiently facilitate progesterone production, which plays a crucial role in ovulation and the following luteinization. Recently, it has become clear that epigenetic regulation such as histone modifications and DNA methylation play a key role in gene expression through the chromatin remodeling of the promoter region. This study reports the in vivo evidence that epigenetic mechanisms including histone modifications, DNA methylation and chromatin remodeling are involved in the rapid changes of StAR and Cyp19a1 gene expression in granulosa cells undergoing luteinization during ovulation.
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Batra JS, Girdhani S, Hlatky L. A Quest to Identify Prostate Cancer Circulating Biomarkers with a Bench-to-Bedside Potential. J Biomark 2014; 2014:321680. [PMID: 26317031 PMCID: PMC4437363 DOI: 10.1155/2014/321680] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 01/07/2014] [Accepted: 01/10/2014] [Indexed: 02/01/2023] Open
Abstract
Prostate cancer (PCA) is a major health concern in current times. Ever since prostate specific antigen (PSA) was introduced in clinical practice almost three decades ago, the diagnosis and management of PCA have been revolutionized. With time, concerns arose as to the inherent shortcomings of this biomarker and alternatives were actively sought. Over the past decade new PCA biomarkers have been identified in tissue, blood, urine, and other body fluids that offer improved specificity and supplement our knowledge of disease progression. This review focuses on superiority of circulating biomarkers over tissue biomarkers due to the advantages of being more readily accessible, minimally invasive (blood) or noninvasive (urine), accessible for sampling on regular intervals, and easily utilized for follow-up after surgery or other treatment modalities. Some of the circulating biomarkers like PCA3, IL-6, and TMPRSS2-ERG are now detectable by commercially available kits while others like microRNAs (miR-21, -221, -141) and exosomes hold potential to become available as multiplexed assays. In this paper, we will review some of these potential candidate circulating biomarkers that either individually or in combination, once validated with large-scale trials, may eventually get utilized clinically for improved diagnosis, risk stratification, and treatment.
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Affiliation(s)
- Jaspreet Singh Batra
- Center of Cancer Systems Biology, GeneSys Research Institute, Tufts University, School of Medicine, 736 Cambridge Street, SEMC-CBR112, Boston, MA 02135, USA
| | - Swati Girdhani
- Center of Cancer Systems Biology, GeneSys Research Institute, Tufts University, School of Medicine, 736 Cambridge Street, SEMC-CBR112, Boston, MA 02135, USA
| | - Lynn Hlatky
- Center of Cancer Systems Biology, GeneSys Research Institute, Tufts University, School of Medicine, 736 Cambridge Street, SEMC-CBR112, Boston, MA 02135, USA
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Abstract
Inorganic arsenic (iAs) poses a major threat to worldwide human health, and yet the molecular mechanisms underlying the toxic effects associated with iAs exposure are not well understood. There is increasing experimental evidence indicating that epigenetic modifications may play a major role in the development of diseases associated with exposure to environmental toxicants. Research in the field has firmly established that iAs exposure is associated with epigenetic alterations including changes in DNA methylation, miRNA abundance, and post-translational histone modifications. Here, we summarize recent studies that have expanded the current knowledge of these relationships. These studies have pinpointed specific regions of the genome and genes that are targets of arsenical-induced epigenetic changes, including those associated with in utero iAs exposure. The recent literature indicates that iAs biotransformation likely plays an important role in the relationship between iAs exposure and the epigenome, in addition to the sex and genetic background of individuals. The research also shows that relatively low to moderate exposure to iAs is associated with epigenetic effects. However, while it is well established that arsenicals can alter components of the epigenome, in many cases, the biological significance of these alterations remains unknown. The manner by which these and future studies may help inform the role of epigenetic modifications in the development of iAs-associated disease is evaluated and the need for functional validation emphasized.
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Affiliation(s)
- Kathryn A. Bailey
- Department of Environmental Sciences and Engineering, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Campus Box 7431, Chapel Hill, NC 27599 USA
| | - Rebecca C. Fry
- Department of Environmental Sciences and Engineering, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Campus Box 7431, Chapel Hill, NC 27599 USA
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Zhang HZ, Xia XY, Zhu F, Shen H, Song K, Shang ZJ. Correlation of deregulated like-acetylglucosaminyl transferase and aberrant α-dystroglycan expression with human tongue cancer metastasis. J Oral Maxillofac Surg 2014; 72:1106-18. [PMID: 24629698 DOI: 10.1016/j.joms.2013.12.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 12/20/2013] [Accepted: 12/26/2013] [Indexed: 11/16/2022]
Abstract
PURPOSE The present study examined the correlation of α-dystroglycan (α-DG) expression and like-acetylglucosaminyl transferase (LARGE) with metastasis of human tongue cancer. MATERIALS AND METHODS Fifty human tongue cancer tissues and 2 tongue squamous cell carcinoma cell lines (CAL27 and SCC4) were involved. Immunohistochemistry was used to detect the expression of α-DG and LARGE. Methylation-specific polymerase chain reaction was performed to assess the methylation status of the LARGE gene promoter. CAL27 and SCC4 cells were transfected with exogenous LARGE and treated with 5-aza-2'-deoxycytidine (Aza-dC), respectively. Glycol sites of α-DG were detected by western blotting. In addition, the laminin overlay assay, cell adhesion assay, and invasion assay were performed. RESULTS Immunohistochemical results showed that decreased expression of VIA4-1 and IIH6 (antibodies that recognize the glycol sites of α-DG) were correlated with the lymph node metastasis of tongue cancer (n = 50; P = .016 and .025, respectively). Decreased LARGE expression and hypermethylation of the LARGE gene promoter were correlated with lymph node metastasis and α-DG glycosylation in human tongue cancer (n = 50; P = .043 and .015 respectively). In addition, LARGE overexpression and Aza-dC treatment actively led to restoration of functional α-DG expression, elevation of laminin binding, and decrease of migratory ability in cancer cells. CONCLUSION The results suggested that absent α-DG expression and LARGE deregulation were closely associated with nodal metastasis of tongue cancer. Aberrant α-DG expression and glycosylation were attributed at least in part to the abnormal epigenetic modification of LARGE, especially the hypermethylation of its promoter.
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Affiliation(s)
- Han-Zhong Zhang
- PhD Student, State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine Ministry of Education, Wuhan University, Wuhan, China
| | - Xiao-Yan Xia
- PhD Student, State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine Ministry of Education, Wuhan University, Wuhan, China
| | - Fei Zhu
- PhD Student, State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine Ministry of Education, Wuhan University, Wuhan, China
| | - Hui Shen
- PhD Student, State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine Ministry of Education, Wuhan University, Wuhan, China
| | - Kai Song
- PhD Student, State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine Ministry of Education, Wuhan University, Wuhan, China
| | - Zheng-Jun Shang
- Professor, State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine Ministry of Education, Wuhan University, Wuhan, China; Department of Oral and Maxillofacial and Head and Neck Oncology, School and Hospital of Stomatology, Wuhan University, Wuhan, China.
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Abstract
Colorectal cancer is the third most common cancer worldwide and arises secondary to the progressive accumulation of genetic and epigenetic alterations in normal colon cells, which results in a polyp-to-cancer progression sequence. It is known that individuals with a personal history of colon adenomas or cancer are at increased risk for metachronous colon neoplasms. One explanation for this increased risk could be field cancerization, which is a phenomenon in which the histologically normal tissue in an organ is primed to undergo transformation. Epigenetic alterations appear to be promising markers for field cancerization. In this review, we discuss field cancerization in the colon and the data supporting the use of methylated DNA as a biomarker for this phenomenon.
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Affiliation(s)
- Yanxin Luo
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, P.R. China, Gastrointestinal Institute, Sun Yat-Sen University, Guangzhou, P.R. China, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA and Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Ming Yu
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, P.R. China, Gastrointestinal Institute, Sun Yat-Sen University, Guangzhou, P.R. China, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA and Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - William M. Grady
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, P.R. China, Gastrointestinal Institute, Sun Yat-Sen University, Guangzhou, P.R. China, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA and Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
- *Corresponding author. Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., D4-100, Seattle, WA 98109, USA. Tel: +1-206-667-1107; Fax: +1-206-667-2917;
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Singh KP. Screening of DNA methylation changes by methylation-sensitive random amplified polymorphic DNA-polymerase chain reaction (MS-RAPD-PCR). Methods Mol Biol 2014; 1105:71-81. [PMID: 24623220 DOI: 10.1007/978-1-62703-739-6_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
While the role of genetic events of DNA mutations in gene expression changes is well established, increasing evidence suggests that epigenetic changes of DNA methylation and histone modifications play important role in the regulation of gene expression. DNA methylation is the most frequent epigenetic alteration observed in mammalian genomes, and it frequently mediates transcriptional repression. Various methods are available for detection of DNA methylation changes. Methylation Sensitive-Random Amplified Polymorphic DNA-Polymerase Chain Reaction (MS-RAPD-PCR) is a restriction enzyme digestion and PCR-based method for analysis of DNA methylation changes. This method is cost-effective, requires simple and basic instrumentation, and therefore can easily be performed in any laboratory with basic setup with a regular DNA thermal cycler and DNA gel electrophoresis system. Other advantages of this method over other methods for DNA methylation analysis are that it requires very less DNA amount and can screen DNA methylation changes globally at genome wide level with high sensitivity. This method has been successfully used to detect DNA methylation changes associated with various human diseases including cancer. This chapter describes the detailed experimental protocol for MS-RAPD-PCR.
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Affiliation(s)
- Kamaleshwar P Singh
- Department of Environmental Toxicology, The Institute of Environmental and Human Health (TIEHH), Texas Tech University, Reese Technology Center Bldg 555, 1207 Gilbert Drive, Lubbock, TX, 79416, USA,
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DNA methylation status of the methylenetetrahydrofolate reductase gene promoter in peripheral blood of end-stage renal disease patients. Mol Biol Rep 2013; 41:683-8. [PMID: 24363223 DOI: 10.1007/s11033-013-2906-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Accepted: 12/12/2013] [Indexed: 12/20/2022]
Abstract
End-stage renal disease (ESRD) is one of the main causes of morbidity and mortality worldwide. DNA methylation is a major epigenetic modification of the genome that has the potential to silence gene expression. Methylenetetrahydrofolate reductase (MTHFR) gene inactivation was recognized as a predisposing factor of hyperhomocysteinemia in renal patients. The current study aimed to determine the methylation status within the MTHFR promoter region in DNA isolated from peripheral blood of ESRD patients and controls and the correlation of this methylation with the clinical and biochemical characteristics in ESRD patients. Ninety-six ESRD patients and 96 healthy ethnically, age and gender matched controls were included within the study. MTHFR promoter methylation was assessed using methylation specific polymerase chain reaction. The frequency of MTHFR methylation was significantly higher in ESRD patients than in controls (P = 0.003), additionally, MTHFR methylation was associated to a decrease in estimated glomerular filtration rate, serum high-density lipoprotein cholesterol level and an increase in both serum total cholesterol and low-density lipoprotein cholesterol levels. Data generated from this study suggest the possible involvement of MTHFR promoter methylation in the pathogenesis of ESRD and support a new dimension of MTHFR inactivation.
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Xie FW, Peng YH, Chen X, Chen X, Li J, Yu ZY, Wang WW, Ouyang XN. Regulation and expression of aberrant methylation on irinotecan metabolic genes CES2, UGT1A1 and GUSB in the in-vitro cultured colorectal cancer cells. Biomed Pharmacother 2013; 68:31-7. [PMID: 24439671 DOI: 10.1016/j.biopha.2013.06.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 06/24/2013] [Indexed: 02/03/2023] Open
Abstract
OBJECTIVE To evaluate the aberrant methylation gene expression related to the irinotecan (CPT-11) metabolic enzymes in different colorectal cancer cell strains; provide new thoughts and measures for reverse of tumor drug resistance. METHODS Studied the aberrant methylation state of CES2, UGT1A1 and GUSB in eight colorectal cancer cell strains through MSP method; and analyze the expression of the target gene after being dealt with DAC. RESULTS UGT1A1 showed methylation in five cell strains, while CES2 and GUSB respectively showed consistent unmethylation or hemimethylation. After being dealt with DAC, CES2 and GUSB mRNA showed different expressions but not significant. The expression quantity of UGT1A1mRNA in the low-expression cell strains increased significantly. The expression of UGT1A1 protein where POSITIVE presented low expression was up-regulated to different degrees. Negative tropism was found in CES2 and UGT1A1. CONCLUSION Methylation in UGT1A1 gene expression silencing as an important mechanism; methylation could provide an effective target for methylation regulation intervening in the treatment of CPT-11. Meanwhile, studies found that the changes in expressions of CES2 and GUSB might be resulted from some unknown target that still existed during the regulation, or from the influence of methylation in the non-core zone of promoters on the gene transcription.
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Affiliation(s)
- Fang-Wei Xie
- Department of Medicine Oncology, Fuzhou General Hospital of Nanjing Military Command, 350025 Fuzhou, Fujian, China.
| | - Yong-Hai Peng
- Department of Medicine Oncology, Fuzhou General Hospital of Nanjing Military Command, 350025 Fuzhou, Fujian, China
| | - Xi Chen
- Department of Medicine Oncology, Fuzhou General Hospital of Nanjing Military Command, 350025 Fuzhou, Fujian, China
| | - Xiong Chen
- Department of Medicine Oncology, Fuzhou General Hospital of Nanjing Military Command, 350025 Fuzhou, Fujian, China
| | - Jie Li
- Department of Medicine Oncology, Fuzhou General Hospital of Nanjing Military Command, 350025 Fuzhou, Fujian, China
| | - Zong-Yang Yu
- Department of Medicine Oncology, Fuzhou General Hospital of Nanjing Military Command, 350025 Fuzhou, Fujian, China
| | - Wen-Wu Wang
- Department of Medicine Oncology, Fuzhou General Hospital of Nanjing Military Command, 350025 Fuzhou, Fujian, China
| | - Xue-Nong Ouyang
- Department of Medicine Oncology, Fuzhou General Hospital of Nanjing Military Command, 350025 Fuzhou, Fujian, China.
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Müller F, Tora L. Chromatin and DNA sequences in defining promoters for transcription initiation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1839:118-28. [PMID: 24275614 DOI: 10.1016/j.bbagrm.2013.11.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 11/11/2013] [Accepted: 11/11/2013] [Indexed: 01/29/2023]
Abstract
One of the key events in eukaryotic gene regulation and consequent transcription is the assembly of general transcription factors and RNA polymerase II into a functional pre-initiation complex at core promoters. An emerging view of complexity arising from a variety of promoter associated DNA motifs, their binding factors and recent discoveries in characterising promoter associated chromatin properties brings an old question back into the limelight: how is a promoter defined? In addition to position-dependent DNA sequence motifs, accumulating evidence suggests that several parallel acting mechanisms are involved in orchestrating a pattern marked by the state of chromatin and general transcription factor binding in preparation for defining transcription start sites. In this review we attempt to summarise these promoter features and discuss the available evidence pointing at their interactions in defining transcription initiation in developmental contexts. This article is part of a Special Issue entitled: Chromatin and epigenetic regulation of animal development.
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Affiliation(s)
- Ferenc Müller
- School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, B15 2TT Edgbaston, Birmingham, UK.
| | - Làszlò Tora
- Cellular Signaling and Nuclear Dynamics Program, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104 CNRS, UdS, INSERM U964, BP 10142, F-67404 Illkirch Cedex, CU de Strasbourg, France; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.
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Diagnostic value of stool DNA testing for multiple markers of colorectal cancer and advanced adenoma: a meta-analysis. CANADIAN JOURNAL OF GASTROENTEROLOGY = JOURNAL CANADIEN DE GASTROENTEROLOGIE 2013; 27:467-75. [PMID: 23936877 DOI: 10.1155/2013/258030] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND OBJECTIVES The diagnostic value of stool DNA (sDNA) testing for colorectal neoplasms remains controversial. To compensate for the lack of large-scale unbiased population studies, a meta-analysis was performed to evaluate the diagnostic value of sDNA testing for multiple markers of colorectal cancer (CRC) and advanced adenoma. METHODS The PubMed, Science Direct, Biosis Review, Cochrane Library and Embase databases were systematically searched in January 2012 without time restriction. Meta-analysis was performed using a random-effects model using sensitivity, specificity, diagnostic OR (DOR), summary ROC curves, area under the curve (AUC), and 95% CIs as effect measures. Heterogeneity was measured using the χ(2) test and Q statistic; subgroup analysis was also conducted. RESULTS A total of 20 studies comprising 5876 individuals were eligible. There was no heterogeneity for CRC, but adenoma and advanced adenoma harboured considerable heterogeneity influenced by risk classification and various detection markers. Stratification analysis according to risk classification showed that multiple markers had a high DOR for the high-risk subgroups of both CRC (sensitivity 0.759 [95% CI 0.711 to 0.804]; specificity 0.883 [95% CI 0.846 to 0.913]; AUC 0.906) and advanced adenoma (sensitivity 0.683 [95% CI 0.584 to 0.771]; specificity 0.918 [95% CI 0.866 to 0.954]; AUC 0.946) but not for the average-risk subgroups of either. In the methylation subgroup, sDNA testing had significantly higher DOR for CRC (sensitivity 0.753 [95% CI 0.685 to 0.812]; specificity 0.913 [95% CI 0.860 to 0.950]; AUC 0.918) and advanced adenoma (sensitivity 0.623 [95% CI 0.527 to 0.712]; specificity 0.926 [95% CI 0.882 to 0.958]; AUC 0.910) compared with the mutation subgroup. There was no significant heterogeneity among studies for subgroup analysis. CONCLUSION sDNA testing for multiple markers had strong diagnostic significance for CRC and advanced adenoma in high-risk subjects. Methylation makers had more diagnostic value than mutation markers.
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Malik RE, Rhodes SJ. The role of DNA methylation in regulation of the murine Lhx3 gene. Gene 2013; 534:272-81. [PMID: 24183897 DOI: 10.1016/j.gene.2013.10.045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 10/09/2013] [Accepted: 10/23/2013] [Indexed: 12/20/2022]
Abstract
LHX3 is a LIM-homeodomain transcription factor with critical roles in pituitary and nervous system development. Mutations in the LHX3 gene are associated with pediatric diseases featuring severe hormone deficiencies, hearing loss, developmental delay, and other symptoms. The mechanisms that govern LHX3/Lhx3 transcription are poorly understood. In this study, we examined the role of DNA methylation in the expression status of the mouse Lhx3 gene. Pituitary cells that do not normally express Lhx3 (Pit-1/0 cells) were treated with 5-aza-2'-deoxycytidine, a demethylating reagent. This treatment leads to activation of Lhx3 gene expression suggesting that methylation contributes to Lhx3 regulation. Treatment of Pit-1/0 pituitary cells with a combination of a demethylating reagent and a histone deacetylase inhibitor led to rapid activation of Lhx3 expression, suggesting possible crosstalk between DNA methylation and histone modification processes. To assess DNA methylation levels, treated and untreated Pit-1/0 genomic DNAs were subjected to bisulfite conversion and sequencing. Treated Pit-1/0 cells had decreased methylation at specific sites in the Lhx3 locus compared to untreated cells. Chromatin immunoprecipitation assays demonstrated interactions between the MeCp2 methyl binding protein and Lhx3 promoter regions in the Pit-1/0 cell line. Overall, this study demonstrates that DNA methylation patterns of the Lhx3 gene are associated with its expression status.
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Affiliation(s)
- Raleigh E Malik
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Simon J Rhodes
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Biology, Indiana University-Purdue University Indianapolis, IN, USA; Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN, USA.
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137
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Li F, Fan YC, Gao S, Sun FK, Yang Y, Wang K. Methylation of serum insulin-like growth factor-binding protein 7 promoter in hepatitis B virus-associated hepatocellular carcinoma. Genes Chromosomes Cancer 2013; 53:90-7. [PMID: 24142767 DOI: 10.1002/gcc.22120] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 09/26/2013] [Indexed: 12/14/2022] Open
Affiliation(s)
- Feng Li
- Department of Hepatology; Qilu Hospital of Shandong University; Jinan China
- Institute of Hepatology; Shandong University; Jinan China
| | - Yu-Chen Fan
- Department of Hepatology; Qilu Hospital of Shandong University; Jinan China
- Institute of Hepatology; Shandong University; Jinan China
| | - Shuai Gao
- Department of Hepatology; Qilu Hospital of Shandong University; Jinan China
| | - Feng-Kai Sun
- Department of Hepatology; Qilu Hospital of Shandong University; Jinan China
| | - Yang Yang
- Department of Hepatology; Qilu Hospital of Shandong University; Jinan China
| | - Kai Wang
- Department of Hepatology; Qilu Hospital of Shandong University; Jinan China
- Institute of Hepatology; Shandong University; Jinan China
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Kang I, Wang Y, Reagan C, Fu Y, Wang MX, Gu LQ. Designing DNA interstrand lock for locus-specific methylation detection in a nanopore. Sci Rep 2013; 3:2381. [PMID: 24135881 PMCID: PMC3798886 DOI: 10.1038/srep02381] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 07/12/2013] [Indexed: 12/31/2022] Open
Abstract
DNA methylation is an important epigenetic regulation of gene transcription. Locus-specific DNA methylation can be used as biomarkers in various diseases including cancer. Many methods have been developed for genome-wide methylation analysis, but molecular diagnotics needs simple tools to determine methylation states at individual CpG sites in a gene fragment. In this report, we utilized the nanopore single-molecule sensor to investigate a base-pair specific metal ion/nucleic acids interaction, and explored its potential application in locus-specific DNA methylation analysis. We identified that divalent Mercury ion (Hg2+) can selectively bind a uracil-thymine mismatch (U-T) in a dsDNA. The Hg2+ binding creates a reversible interstrand lock, called MercuLock, which enhances the hybridization strength by two orders of magnitude. Such MercuLock cannot be formed in a 5-methylcytosine-thymine mismatch (mC-T). By nanopore detection of dsDNA stability, single bases of uracil and 5-methylcytosine can be distinguished. Since uracil is converted from cytosine by bisulfite treatment, cytosine and 5′-methylcytosine can be discriminated. We have demonstrated the methylation analysis of multiple CpGs in a p16 gene CpG island. This single-molecule assay may have potential in detection of epigenetic cancer biomarkers in biofluids, with an ultimate goal for early diagnosis of cancer.
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Affiliation(s)
- Insoon Kang
- Department of Bioengineering and Dalton Cardiovascular Research Center
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Sun J, Lin Y, Wu J. Long non-coding RNA expression profiling of mouse testis during postnatal development. PLoS One 2013; 8:e75750. [PMID: 24130740 PMCID: PMC3794988 DOI: 10.1371/journal.pone.0075750] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 08/19/2013] [Indexed: 02/07/2023] Open
Abstract
Mammalian testis development and spermatogenesis play critical roles in male fertility and continuation of a species. Previous research into the molecular mechanisms of testis development and spermatogenesis has largely focused on the role of protein-coding genes and small non-coding RNAs, such as microRNAs and piRNAs. Recently, it has become apparent that large numbers of long (>200 nt) non-coding RNAs (lncRNAs) are transcribed from mammalian genomes and that lncRNAs perform important regulatory functions in various developmental processes. However, the expression of lncRNAs and their biological functions in post-natal testis development remain unknown. In this study, we employed microarray technology to examine lncRNA expression profiles of neonatal (6-day-old) and adult (8-week-old) mouse testes. We found that 8,265 lncRNAs were expressed above background levels during post-natal testis development, of which 3,025 were differentially expressed. Candidate lncRNAs were identified for further characterization by an integrated examination of genomic context, gene ontology (GO) enrichment of their associated protein-coding genes, promoter analysis for epigenetic modification, and evolutionary conservation of elements. Many lncRNAs overlapped or were adjacent to key transcription factors and other genes involved in spermatogenesis, such as Ovol1, Ovol2, Lhx1, Sox3, Sox9, Plzf, c-Kit, Wt1, Sycp2, Prm1 and Prm2. Most differentially expressed lncRNAs exhibited epigenetic modification marks similar to protein-coding genes and tend to be expressed in a tissue-specific manner. In addition, the majority of differentially expressed lncRNAs harbored evolutionary conserved elements. Taken together, our findings represent the first systematic investigation of lncRNA expression in the mammalian testis and provide a solid foundation for further research into the molecular mechanisms of lncRNAs function in mammalian testis development and spermatogenesis.
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Affiliation(s)
- Jin Sun
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Lin
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ji Wu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan, Ningxia, China
- * E-mail:
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141
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Bajpai M, Kessel R, Bhagat T, Nischal S, Yu Y, Verma A, Das KM. High resolution integrative analysis reveals widespread genetic and epigenetic changes after chronic in-vitro acid and bile exposure in Barrett's epithelium cells. Genes Chromosomes Cancer 2013; 52:1123-32. [PMID: 24123713 DOI: 10.1002/gcc.22106] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 07/31/2013] [Accepted: 08/01/2013] [Indexed: 12/12/2022] Open
Abstract
Barrett's epithelium (BE) is a premalignant condition resulting from chronic gastroesophageal reflux that may progress to esophageal adenocarcinoma (EAC). Early intervention holds promise in preventing BE progression. However, identification of high-risk BE patients remains challenging due to inadequate biomarkers for early diagnosis. We investigated the effect of prolonged chronic acid and bile exposure on transcriptome, methylome, and mutatome of cells in an in-vitro BE carcinogenesis (BEC) model. Twenty weeks acid and bile exposed cells from the BEC model (BEC20w) were compared with their naïve predecessors HiSeq Illumina based RNA sequencing was performed on RNA from both the cells for gene expression and mutational analysis. HELP Tagging Assay was performed for DNA methylation analysis. Ingenuity pathway, Gene Ontology, and KEGG PATHWAY analyses were then performed on datasets. Widespread aberrant genetic and epigenetic changes were observed in the BEC20w cells. Combinatorial analyses revealed 433 from a total of 863 downregulated genes had accompanying hypermethylation of promoters. Simultaneously, 690 genes from a total of 1,492 were upregulated with accompanying promoter hypomethylation. In addition, 763 mutations were identified on 637 genes. Ingenuity pathway analysis, Gene Ontology, and KEGG PATHWAY analyses associated the genetic and epigenetic changes in BEC20w cells with cellular and biological functions. Integration of high resolution comparative analyses of naïve BAR-T and BEC20w cells revealed striking genetic and epigenetic changes induced by chronic acid and bile exposure that may disrupt normal cellular functions and promote carcinogenesis. This novel study reveals several potential targets for future biomarkers and therapeutic development.
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Affiliation(s)
- Manisha Bajpai
- Division of Gastroenterology and Hepatology, Department of Medicine, RUTGERS Robert Wood Johnson Medical School, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ
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Abstract
Spinal cord injury results from an insult inflicted on the spinal cord that usually encompasses its 4 major functions (motor, sensory, autonomic, and reflex). The type of deficits resulting from spinal cord injury arise from primary insult, but their long-term severity is due to a multitude of pathophysiological processes during the secondary phase of injury. The failure of the mammalian spinal cord to regenerate and repair is often attributed to the very feature that makes the central nervous system special-it becomes so highly specialized to perform higher functions that it cannot effectively reactivate developmental programs to re-build novel circuitry to restore function after injury. Added to this is an extensive gliotic and immune response that is essential for clearance of cellular debris, but also lays down many obstacles that are detrimental to regeneration. Here, we discuss how the mature chromatin state of different central nervous system cells (neural, glial, and immune) may contribute to secondary pathophysiology, and how restoring silenced developmental gene expression by altering histone acetylation could stall secondary damage and contribute to novel approaches to stimulate endogenous repair.
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Affiliation(s)
- Elisa M. York
- Department of Zoology (Life Sciences Institute), Brain Research Institute and International Collaboration on Repair Discoveries (iCORD), University of British Columbia, 2350 Health Sciences Blvd, V6T 1Z3 Vancouver, Canada
| | - Audrey Petit
- Department of Zoology (Life Sciences Institute), Brain Research Institute and International Collaboration on Repair Discoveries (iCORD), University of British Columbia, 2350 Health Sciences Blvd, V6T 1Z3 Vancouver, Canada
| | - A. Jane Roskams
- Department of Zoology (Life Sciences Institute), Brain Research Institute and International Collaboration on Repair Discoveries (iCORD), University of British Columbia, 2350 Health Sciences Blvd, V6T 1Z3 Vancouver, Canada
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143
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Poloni A, Goteri G, Zizzi A, Serrani F, Trappolini S, Costantini B, Mariani M, Olivieri A, Catarini M, Centurioni R, Alesiani F, Giantomassi F, Stramazzotti D, Biagetti S, Alfonsi S, Berardinelli E, Leoni P. Prognostic role of immunohistochemical analysis of 5 mc in myelodysplastic syndromes. Eur J Haematol 2013; 91:219-227. [DOI: 10.1111/ejh.12145] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2013] [Indexed: 12/19/2022]
Affiliation(s)
- Antonella Poloni
- Clinica di Ematologia; Dipartimento di Scienze Cliniche e Molecolari; Università Politecnica Marche; Ancona; Italy
| | - Gaia Goteri
- Anatomia Patologica; Dipartimento di Neuroscienze; Università Politecnica Marche; Ancona; Italy
| | - Antonio Zizzi
- Anatomia Patologica; Dipartimento di Neuroscienze; Università Politecnica Marche; Ancona; Italy
| | - Federica Serrani
- Clinica di Ematologia; Dipartimento di Scienze Cliniche e Molecolari; Università Politecnica Marche; Ancona; Italy
| | - Silvia Trappolini
- Clinica di Ematologia; Dipartimento di Scienze Cliniche e Molecolari; Università Politecnica Marche; Ancona; Italy
| | - Benedetta Costantini
- Clinica di Ematologia; Dipartimento di Scienze Cliniche e Molecolari; Università Politecnica Marche; Ancona; Italy
| | - Marianna Mariani
- Clinica di Ematologia; Dipartimento di Scienze Cliniche e Molecolari; Università Politecnica Marche; Ancona; Italy
| | - Attilio Olivieri
- Clinica di Ematologia; Dipartimento di Scienze Cliniche e Molecolari; Università Politecnica Marche; Ancona; Italy
| | | | | | | | - Federica Giantomassi
- Anatomia Patologica; Dipartimento di Neuroscienze; Università Politecnica Marche; Ancona; Italy
| | - Daniela Stramazzotti
- Anatomia Patologica; Dipartimento di Neuroscienze; Università Politecnica Marche; Ancona; Italy
| | - Simona Biagetti
- Anatomia Patologica; Dipartimento di Neuroscienze; Università Politecnica Marche; Ancona; Italy
| | - Simona Alfonsi
- Anatomia Patologica; Dipartimento di Neuroscienze; Università Politecnica Marche; Ancona; Italy
| | - Eleonora Berardinelli
- Clinica di Ematologia; Dipartimento di Scienze Cliniche e Molecolari; Università Politecnica Marche; Ancona; Italy
| | - Pietro Leoni
- Clinica di Ematologia; Dipartimento di Scienze Cliniche e Molecolari; Università Politecnica Marche; Ancona; Italy
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Zhao Y, Chen M, Su L, Wang T, Liu S, Yang H. Molecular cloning and expression-profile analysis of sea cucumber DNA (Cytosine-5)-methyltransferase 1 and methyl-CpG binding domain type 2/3 genes during aestivation. Comp Biochem Physiol B Biochem Mol Biol 2013; 165:26-35. [DOI: 10.1016/j.cbpb.2013.02.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Revised: 02/22/2013] [Accepted: 02/25/2013] [Indexed: 10/27/2022]
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Li X, Yao X, Wang Y, Hu F, Wang F, Jiang L, Liu Y, Wang D, Sun G, Zhao Y. MLH1 promoter methylation frequency in colorectal cancer patients and related clinicopathological and molecular features. PLoS One 2013; 8:e59064. [PMID: 23555617 PMCID: PMC3612054 DOI: 10.1371/journal.pone.0059064] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 02/12/2013] [Indexed: 02/07/2023] Open
Abstract
Purpose To describe the frequency of MLH1 promoter methylation in colorectal cancer (CRC); to explore the associations between MLH1 promoter methylation and clinicopathological and molecular factors using a systematic review and meta-analysis. Methods A literature search of the PubMed and Embase databases was conducted to identify relevant articles published up to September 7, 2012 that described the frequency of MLH1 promoter methylation or its associations with clinicopathological and molecular factors in CRC. The pooled frequency, odds ratio (OR) and 95% confidence intervals (95% CI) were calculated. Results The pooled frequency of MLH1 promoter methylation in unselected CRC was 20.3% (95% CI: 16.8–24.1%). They were 18.7% (95% CI: 14.7–23.6%) and 16.4% (95% CI: 11.9–22.0%) in sporadic and Lynch syndrome (LS) CRC, respectively. Significant associations were observed between MLH1 promoter methylation and gender (pooled OR = 1.641, 95% CI: 1.215–2.215; P = 0.001), tumor location (pooled OR = 3.804, 95% CI: 2.715–5.329; P<0.001), tumor differentiation (pooled OR = 2.131, 95% CI: 1.464–3.102; P<0.001), MSI (OR: 27.096, 95% CI: 13.717–53.526; P<0.001). Significant associations were also observed between MLH1 promoter methylation and MLH1 protein expression, BRAF mutation (OR = 14.919 (95% CI: 6.427–34.631; P<0.001) and 9.419 (95% CI: 2.613–33.953; P = 0.001), respectively). Conclusion The frequency of MLH1 promoter methylation in unselected CRC was 20.3%. They were 18.7% in sporadic CRC and 16.4% in LS CRC, respectively. MLH1 promoter methylation may be significantly associated with gender, tumor location, tumor differentiation, MSI, MLH1 protein expression, and BRAF mutation.
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Affiliation(s)
- Xia Li
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang Province, P.R. China
| | - Xiaoping Yao
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang Province, P.R. China
| | - Yibaina Wang
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang Province, P.R. China
| | - Fulan Hu
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang Province, P.R. China
| | - Fan Wang
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang Province, P.R. China
| | - Liying Jiang
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang Province, P.R. China
| | - Yupeng Liu
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang Province, P.R. China
| | - Da Wang
- Department of Science and Technology Administration, Harbin Medical University, Harbin, Heilongjiang Province, P.R. China
| | - Guizhi Sun
- Department of Surgery, Cancer Hospital of Harbin Medical University, Harbin, Heilongjiang Province, P.R. China
| | - Yashuang Zhao
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang Province, P.R. China
- * E-mail:
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Abstract
BACKGROUND Osteoarthritis (OA) is a frustrating disease for both patient and physician because neither cause nor cure is known and there are currently no disease-modifying drugs. OBJECTIVE To review current therapeutic approaches as well as new findings regarding OA pathoetiology that could form the basis of future direction for the development of drugs to prevent or slow down disease progression. METHODS After reviewing disease progression in human OA, as demonstrated by histological analyses, the reasons for cartilage erosion are explored and possible therapeutic approaches are highlighted. RESULTS/CONCLUSIONS OA may be an epigenetic disease. This new concept can explain many aspects of the disease and provide reasons why therapeutic approaches until now have met with little success.
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Affiliation(s)
- Helmtrud I Roach
- University of Southampton General Hospital, Bone & Joint Research Group, Southampton SO16 6YD, UK +44 023 8079 4316 ; +44 023 8079 5256 ;
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147
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Epigenetics in fertilization and preimplantation embryo development. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 113:423-32. [PMID: 23454467 DOI: 10.1016/j.pbiomolbio.2013.02.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Revised: 01/10/2013] [Accepted: 02/20/2013] [Indexed: 12/30/2022]
Abstract
Epigenetic reprogramming of the parental genomes upon fertilization is required for proper embryonic development. It has long been appreciated that asymmetric distribution of histone modifications as well as differences in the level of DNA methylation exist between the parental pronuclei in mammalian zygotes and during preimplantation development. The speed at which the paternal genome is demethylated after entering the oocyte and the fact that rapid demethylation occurs in the absence of DNA replication have led many to hypothesize that a DNA demethylase must exist. However, such an enzyme has not been found. That the genome of mammalian preimplantation embryos undergo a wave of global demethylation was first reported 25 years ago but only in the past three years has data surfaced that can partially explain the elusive nature of this phenomenon. In addition to the global reorganization of the methylation and histone modification patterns, oocyte development prior to germinal vesicle breakdown involves the production of numerous small RNA, including miRNA. Despite their presence, miRNA functional activity is thought to be limited in the mature mouse oocyte. Additionally, molecular signatures in the 3' untranslated region of maternally expressed transcripts may impact mRNA stability during the transcriptionally quiescent period following germinal vesicle breakdown and prior to the maternal to zygote transition. In this review, we reference some of the recent works which attempt to shed light into the importance of the dynamic epigenetic landscape observed during oocyte maturation and preimplantation embryo development in mammals.
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Liu ZG, Chen HY, Cheng JJ, Chen ZP, Li XN, Xia YF. Relationship between methylation status of ERCC1 promoter and radiosensitivity in glioma cell lines. Cell Biol Int 2013; 33:1111-7. [DOI: 10.1016/j.cellbi.2009.07.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Revised: 05/03/2009] [Accepted: 07/25/2009] [Indexed: 12/01/2022]
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Lee SE, Kim SJ, Yoon HJ, Yu SY, Yang H, Jeong SI, Hwang SY, Park CS, Park YS. Genome-wide profiling in melatonin-exposed human breast cancer cell lines identifies differentially methylated genes involved in the anticancer effect of melatonin. J Pineal Res 2013; 54:80-8. [PMID: 22856590 DOI: 10.1111/j.1600-079x.2012.01027.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 06/22/2012] [Indexed: 01/07/2023]
Abstract
Epigenetic alterations have emerged as an important mechanism involved in tumorigenesis. The epigenetic impact of DNA methylation in various types of human cancer is not completely understood. Previously, we observed melatonin-induced differential expression of miRNA and miRNA-related genes in human breast cancer cell lines that indicated an anticancer effect of melatonin. In this report, we further characterized epigenetic changes in melatonin-exposed MCF-7 cells through the analysis of DNA methylation profiles in breast cancer cells to provide new insights into the potential mechanisms of the anticancer effect of melatonin. Microarray-based DNA methylation and gene expression profiling were carried out using human breast cancer cell lines. We further identified a number of mRNAs whose expression levels show an inverse correlation with DNA methylation levels. The mRNA expression levels and methylation status of candidate genes in melatonin-exposed cells were confirmed by real-time quantitative PCR and bisulfite PCR. This approach led to the detection of cancer-related genes, which were oncogenic genes, including EGR3 and POU4F2/Brn-3b were down-regulated, while the tumor suppressor gene, GPC3, was up-regulated by 1 nm melatonin-treated MCF-7 cells. Our results provide detailed insights into the DNA methylation patterns induced by melatonin and suggest a potential mechanism of the anticancer effect of aberrant DNA methylation in melatonin-treated breast cancer cells.
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Affiliation(s)
- Seung Eun Lee
- Department of Microbiology, School of Medicine, Kyung Hee University, Seoul, Korea
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Lee L, Asada H, Kizuka F, Tamura I, Maekawa R, Taketani T, Sato S, Yamagata Y, Tamura H, Sugino N. Changes in histone modification and DNA methylation of the StAR and Cyp19a1 promoter regions in granulosa cells undergoing luteinization during ovulation in rats. Endocrinology 2013. [PMID: 23183184 DOI: 10.1210/en.2012-1610] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The ovulatory LH surge induces rapid up-regulation of steroidogenic acute regulatory (StAR) protein and rapid down-regulation of aromatase (Cyp19a1) in granulosa cells (GCs) undergoing luteinization during ovulation. This study investigated in vivo whether epigenetic mechanisms including histone modifications are involved in the rapid changes of StAR and Cyp19a1 gene expression. GCs were obtained from rats treated with equine chorionic gonadotropin (CG) before (0 h) and after human (h)CG injection. StAR mRNA levels rapidly increased after hCG injection, reached a peak at 4 h, and then remained higher compared with 0 h until 12 h. Cyp19a1 mRNA levels gradually decreased after hCG injection and reached their lowest level at 12 h. A chromatin immunoprecipitation assay revealed that levels of histone-H4 acetylation (Ac-H4) and trimethylation of histone-H3 lysine-4 (H3K4me3) increased whereas H3K9me3 and H3K27me3 decreased in the StAR promoter after hCG injection. On the other hand, the levels of Ac-H3 and -H4 and H3K4me3 decreased, and H3K27me3 increased in the Cyp19a1 promoter after hCG injection. Chromatin condensation, which was analyzed using deoxyribonuclease I, decreased in the StAR promoter and increased in the Cyp19a1 promoter after hCG injection. A chromatin immunoprecipitation assay also showed that binding activities of CAATT/enhancer-binding protein β to the StAR promoter increased and binding activities of phosphorylated-cAMP response element binding protein to the Cyp19a1 promoter decreased after hCG injection. These results provide in vivo evidence that histone modifications are involved in the rapid changes of StAR and Cyp19a1 gene expression by altering chromatin structure of the promoters in GCs undergoing luteinization during ovulation.
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Affiliation(s)
- Lifa Lee
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube 755-8505, Japan
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