DNA methylation patterns of RAR ‐β2 and RASSF1A gene promoters in FNAB samples from Greek population with benign or malignant breast lesions

2020 ◽  
Vol 49 (1) ◽  
pp. 153-164
Author(s):  
Niki Kougioumtsidou ◽  
Eleftherios Vavoulidis ◽  
Maria Nasioutziki ◽  
Marianthi Symeonidou ◽  
Georgios Chrysostomos Pratilas ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Greek Population ◽  
Breast Lesions ◽  
Gene Promoters ◽  
Rassf1a Gene ◽  
Malignant Breast ◽  
Methylation Patterns

Abstract 40: Disturbed Flow Alters Genomewide DNA Methylation Patterns, Regulating Endothelial Gene Expression and Atherosclerosis

2014 ◽  
Vol 34 (suppl_1) ◽  
Author(s):  
Jessilyn Dunn ◽  
Haiwei Qiu ◽  
Soyeon Kim ◽  
Daudi Jjingo ◽  
Ryan Hoffman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Dna Methyltransferase ◽  
Methylation Status ◽  
Western Diet ◽  
Dependent Manner ◽  
Gene Promoters ◽  
Genome Wide ◽  
Methylation Patterns ◽  
Endothelial Gene Expression

Atherosclerosis preferentially occurs in arterial regions of disturbed blood flow (d-flow), which alters gene expression, endothelial function, and atherosclerosis. Here, we show that d-flow regulates genome-wide DNA methylation patterns in a DNA methyltransferase (DNMT)-dependent manner. We found that d-flow induced expression of DNMT1, but not DNMT3a or DNMT3b, in mouse arterial endothelium in vivo and in cultured endothelial cells by oscillatory shear (OS) compared to unidirectional laminar shear in vitro. The DNMT inhibitor 5-Aza-2’deoxycytidine (5Aza) or DNMT1 siRNA significantly reduced OS-induced endothelial inflammation. Moreover, 5Aza reduced lesion formation in two atherosclerosis models using ApoE-/- mice (western diet for 3 months and the partial carotid ligation model with western diet for 3 weeks). To identify the 5Aza mechanisms, we conducted two genome-wide studies: reduced representation bisulfite sequencing (RRBS) and transcript microarray using endothelial-enriched gDNA and RNA, respectively, obtained from the partially-ligated left common carotid artery (LCA exposed to d-flow) and the right contralateral control (RCA exposed to s-flow) of mice treated with 5Aza or vehicle. D-flow induced DNA hypermethylation in 421 gene promoters, which was significantly prevented by 5Aza in 335 genes. Systems biological analyses using the RRBS and the transcriptome data revealed 11 mechanosensitive genes whose promoters were hypermethylated by d-flow but rescued by 5Aza treatment. Of those, five genes contain hypermethylated cAMP-response-elements in their promoters, including the transcription factors HoxA5 and Klf3. Their methylation status could serve as a mechanosensitive master switch in endothelial gene expression. Our results demonstrate that d-flow controls epigenomic DNA methylation patterns in a DNMT-dependent manner, which in turn alters endothelial gene expression and induces atherosclerosis.

scholarly journals Ultradeep Bisulfite Sequencing Analysis of DNA Methylation Patterns in Multiple Gene Promoters by 454 Sequencing

2007 ◽  
Vol 67 (18) ◽  
pp. 8511-8518 ◽  
Author(s):  
Kristen H. Taylor ◽  
Robin S. Kramer ◽  
J. Wade Davis ◽  
Juyuan Guo ◽  
Deiter J. Duff ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
454 Sequencing ◽  
Sequencing Analysis ◽  
Gene Promoters ◽  
Multiple Gene ◽  
Methylation Patterns ◽  
Bisulfite Sequencing Analysis

scholarly journals Induced Methylation in Plants as a Crop Improvement Tool: Progress and Perspectives

Agronomy ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1484
Author(s):  
Clémentine Mercé ◽  
Philipp E. Bayer ◽  
Cassandria Tay Fernandez ◽  
Jacqueline Batley ◽  
David Edwards
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Epigenetic Modification ◽  
Crop Improvement ◽  
Regulation Of Gene Expression ◽  
Gene Promoters ◽  
Control Of Gene Expression ◽  
Underlying Mechanisms ◽  
Successive Generations ◽  
Methylation Patterns

The methylation of gene promoters is an epigenetic process that can have a major impact on plant phenotypes through its control of gene expression. This phenomenon can be observed as a response to stress, such as drought, cold/heat stress or pathogen infection. The transgenerational heritability of DNA methylation marks could enable breeders to fix beneficial methylation patterns in crops over successive generations. These properties of DNA methylation, its impact on the phenotype and its heritability, could be used to support the accelerated breeding of improved crop varieties. Induced DNA methylation has the potential to complement the existing plant breeding process, supporting the introduction of desirable characteristics in crops within a single generation that persist in its progeny. Therefore, it is important to understand the underlying mechanisms involved in the regulation of gene expression through DNA methylation and to develop methods for precisely modulating methylation patterns for crop improvement. Here we describe the currently available epigenetic editing tools and their advantages and limitations in the domain of crop breeding. Finally, we discuss the biological and legislative limitations currently restricting the development of epigenetic modification as a crop improvement tool.

Weighted Gene Coregulation Network Analysis of Promoter DNA Methylation on All-Cause Mortality in Old-Aged Birth Cohorts Finds Modules of High-Risk Associated Biomarkers

2020 ◽  
Vol 75 (12) ◽  
pp. 2249-2257 ◽  
Author(s):  
Jesper B Lund ◽  
Shuxia Li ◽  
Jan Baumbach ◽  
Kaare Christensen ◽  
Weilong Li ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Network Analysis ◽  
Association Studies ◽  
Gene Clusters ◽  
Gene Promoters ◽  
Older Individuals ◽  
Birth Cohorts ◽  
Risk Of Death ◽  
All Cause Mortality ◽  
Methylation Patterns

Abstract Overall or all-cause mortality is a key measure of health in a population. Multiple epigenome-wide association studies have been conducted on all-cause mortality with limited significant findings and low replication. To elucidate the coregulated DNA methylation patterns associated with all-cause mortality, we conducted a weighted DNA methylation coregulation network analysis on whole-blood samples of 1,425 older individuals from the Lothian Birth Cohorts of 1921 and 1936. Our network-based analysis defined coregulated DNA methylation patterns in gene promoters into clusters or modules whose correlation with all-cause mortality was assessed by survival analysis. We found two significant modules or gene clusters associated with all-cause mortality in LBC1921 based on their eigengenes; one negatively correlated (p = 8.14E-03, 698 genes) and one positively correlated (p = 4.26E-02, 1,431 genes) with the risk of death. The two modules were replicated in LBC1936 with the same directions of correlation (p = 6.35E-02 and p = 3.64E-02, respectively). Furthermore, the modules revealed 32 genes associated with all-cause mortality (FDR < 0.05) linked to various diseases, including cancer and diabetes. Additionally, we performed pathway analysis and found 22 pathways (FDR < 0.05), including a pathway for taste transduction, which has been shown to be associated with poor prognosis in acutely hospitalized patients, and several pathways were linked to different types of cancer. The results from our network analysis show that DNA methylation of multiple genes could have been coregulated in an association with the overall risk of death. The identified epigenetic markers might help with our understanding of the molecular basis of all-cause mortality and general health.

201Tl Scintigraphy in the Evaluation of Palpable and Nonpalpable Breast Lesions: Correlation with Mammography and Ultrasonography

1997 ◽  
Vol 36 (08) ◽  
pp. 282-288 ◽  
Author(s):  
T. Atasever ◽  
A. Özdemir ◽  
I. Öznur ◽  
N. I. Karabacak ◽  
N. Gökçora ◽  
...  
Keyword(s):  
Final Diagnosis ◽  
Lower Sensitivity ◽  
Breast Lesions ◽  
Breast Cancers ◽  
Combined Use ◽  
Malignant Breast ◽  
Malignant Lesions ◽  
Benign Breast Lesions ◽  
Palpable Breast ◽  
Metastatic Sites

Summary Aim: Our goal was to determine the clinical usefulness of TI-201 to identify breast cancer in patients with suspicious breast lesions on clinical examination, and/or abnormal radiologic (mammography and/or ultrasonography) findings. Methods: TI-201 scintigraphy were performed in sixty-eight patients with 70 breast abnormalities (51 palpable, 19 nonpalpable) and compared with mammography and ultrasonography (US). Early (15 min) and late (3 h) images of the breasts were obtained following the injection of 111 MBq (3 mCi) of TI-201. Visual and semiquantitative interpretation was performed. Results: Final diagnosis confirmed 52 malignant breast lesions and 18 benign conditions. TI-201 visualized 47 of 52 (90%) overall malignant lesions. Thirty-eight of 40 (95%) palpable and 9 of 12 (75%) nonpalpable breast cancers were detected by TI-201 scintigraphy. The smallest mass lesion detected by TI-201 measured 1.5x1.0 cm. Eleven breast lesions were interpreted as indeterminate by mammography and/or sonography. TI-201 scintigraphy excluded malignancy in 7 of 8 (88%) patients with benign breast lesions interpreted as indeterminate. Five of the 18 (28%) benign breast lesions showed TI-201 uptake. None of the fibroadenoma and fibrocystic changes accumulated TI-201. TI-201 scintigraphy, mammography and ultrasonography showed 90%, 92%, 85% overall sensitivity and 72%, 56%, 61% overall specificity respectively. Twenty-one of the 28 (75%) axillary nodal metastatic sites were also detected by TI-201. In malignant and benign lesions, early and late lesion/contralateral normal side (L/N) ratios were 1.58 ± 0.38 (mean ± SD) and 1.48 ± 0.32 (p >0.05), 1.87 ± 0.65 and 1.34 ± 0.20 (p<0.05) respectively. The mean early and late L/N ratios of malignant and benign groups did not show statistical difference (p>0.05). Conclusion: Overall, TI-201 scintigraphy was the most specific of the three methods and yielded favourable results in palpable breast cancers, while it showed lower sensitivity in nonpalpable cancers and axillary metastases. Combined use of TI-201 scintigraphy with mammography and US seems to be useful in difficult cases, such as dense breasts and indeterminate breast lesions.

Examination of the dynamics of global DNA methylation pattern establishment during spermatogenesiss

2007 ◽  
Vol 30 (4) ◽  
pp. 90
Author(s):  
Kirsten Niles ◽  
Sophie La Salle ◽  
Christopher Oakes ◽  
Jacquetta Trasler
Keyword(s):  
Dna Methylation ◽  
Germ Cell ◽  
Germ Cells ◽  
Epigenetic Modification ◽  
Methylation Pattern ◽  
Chromosome 9 ◽  
Specific Gene ◽  
Global Methylation ◽  
Dna Methylation Pattern ◽  
Methylation Patterns

Background: DNA methylation is an epigenetic modification involved in gene expression, genome stability, and genomic imprinting. In the male, methylation patterns are initially erased in primordial germ cells (PGCs) as they enter the gonadal ridge; methylation patterns are then acquired on CpG dinucleotides during gametogenesis. Correct pattern establishment is essential for normal spermatogenesis. To date, the characterization and timing of methylation pattern acquisition in PGCs has been described using a limited number of specific gene loci. This study aimed to describe DNA methylation pattern establishment dynamics during male gametogenesis through global methylation profiling techniques in a mouse model. Methods: Using a chromosome based approach, primers were designed for 24 regions spanning chromosome 9; intergenic, non-repeat, non-CpG island sequences were chosen for study based on previous evidence that these types of sequences are targets for testis-specific methylation events. The percent methylation was determined in each region by quantitative analysis of DNA methylation using real-time PCR (qAMP). The germ cell-specific pattern was determined by comparing methylation between spermatozoa and liver. To examine methylation in developing germ cells, spermatogonia from 2 day- and 6 day-old Oct4-GFP (green fluorescent protein) mice were isolated using fluorescence activated cell sorting. Results: As compared to liver, four loci were hypomethylated and five loci were hypermethylated in spermatozoa, supporting previous results indicating a unique methylation pattern in male germ cells. Only one region was hypomethylated and no regions were hypermethylated in day 6 spermatogonia as compared to mature spermatozoa, signifying that the bulk of DNA methylation is established prior to type A spermatogonia. The methylation in day 2 spermatogonia, germ cells that are just commencing mitosis, revealed differences of 15-20% compared to day 6 spermatogonia at five regions indicating that the most crucial phase of DNA methylation acquisition occurs prenatally. Conclusion: Together, these studies provide further evidence that germ cell methylation patterns differ from those in somatic tissues and suggest that much of methylation at intergenic sites is acquired during prenatal germ cell development. (Supported by CIHR)

Amplification of HER-2 Gene in Benign and Malignant Breast Lesions in a Sample of Iraqi Women

2017 ◽  
Vol 13 (2) ◽  
pp. 35-39
Author(s):  
Maysoon Abdul-Ameer Ahmed Al-Salman ◽  
◽  
Risala Hussain Allami ◽  
Lamyaa H. M. Al-Ibrahimi
Keyword(s):  
Breast Lesions ◽  
Malignant Breast ◽  
Iraqi Women ◽  
Her 2
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