scholarly journals DNA Methylation and Gene Expression Profiling of Ewing Sarcoma Primary Tumors Reveal Genes That Are Potential Targets of Epigenetic Inactivation

Sarcoma ◽  
2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Nikul Patel ◽  
Jennifer Black ◽  
Xi Chen ◽  
A. Mario Marcondes ◽  
William M. Grady ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Cell Lines ◽  
Ewing Sarcoma ◽  
Methylation Status ◽  
Primary Cultures ◽  
Human Mesenchymal Stem Cell ◽  
Primary Tumors ◽  
Hypermethylated Genes

The role of aberrant DNA methylation in Ewing sarcoma is not completely understood. The methylation status of 503 genes in 52 formalin-fixed paraffin-embedded EWS tumors and 3 EWS cell lines was compared to human mesenchymal stem cell primary cultures (hMSCs) using bead chip methylation analysis. Relative expression of methylated genes was assessed in 5-Aza-2-deoxycytidine-(5-AZA)-treated EWS cell lines and in a cohort of primary EWS samples and hMSCs by gene expression and quantitative RT-PCR. 129 genes demonstrated statistically significant hypermethylation in EWS tumors compared to hMSCs. Thirty-six genes were profoundly methylated in EWS and unmethylated in hMSCs. 5-AZA treatment of EWS cell lines resulted in upregulation of expression of hundreds of genes including 162 that were increased by at least 2-fold. The expression of 19 of 36 candidate hypermethylated genes was increased following 5-AZA. Analysis of gene expression from an independent cohort of tumors confirmed decreased expression of six of nineteen hypermethylated genes (AXL, COL1A1, CYP1B1, LYN, SERPINE1,) andVCAN. Comparing gene expression and DNA methylation analyses proved to be an effective way to identify genes epigenetically regulated in EWS. Further investigation is ongoing to elucidate the role of these epigenetic alterations in EWS pathogenesis.

scholarly journals Title Page Title: The role of DNA methylation in the accumulation of iridoid glycosides in Rehmannia glutinosa

2021 ◽  
Author(s):  
Tianyu Dong ◽  
Xiaoyan Wei ◽  
Qianting Qi ◽  
Peilei Chen ◽  
Yanqing Zhou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Secondary Metabolites ◽  
Iridoid Glycosides ◽  
Methylation Status ◽  
Plant Secondary Metabolites ◽  
Dna Demethylation ◽  
Terpene Biosynthesis ◽  
The Relationship

Abstract Background: Epigenetic regulation plays a significant role in the accumulation of plant secondary metabolites. The terpenoids are the most abundant in the secondary metabolites of plants, iridoid glycosides belong to monoterpenoids which is one of the main medicinal components of R.glutinosa. At present, study on iridoid glycosides mainly focuses on its pharmacology, accumulation and distribution, while the mechanism of its biosynthesis and the relationship between DNA methylation and plant terpene biosynthesis are seldom reports. Results: The research showed that the expression of DXS, DXR, 10HGO, G10H, GPPS and accumulation of iridoid glycosides increased at first and then decreased with the maturity of R.glutinosa, and under different concentrations of 5-azaC, the expression of DXS, DXR, 10HGO, G10H, GPPS and the accumulation of total iridoid glycosides were promoted, the promotion effect of low concentration (15μM-50μM) was more significant, the content of genomic DNA 5mC decreased significantly, the DNA methylation status of R.glutinosa genomes was also changed. DNA demethylation promoted gene expression and increased the accumulation of iridoid glycosides, but excessive demethylation inhibited gene expression and decreased the accumulation of iridoid glycosides. Conclusion: The analysis of DNA methylation, gene expression, and accumulation of iridoid glycoside provides insights into accumulation of terpenoids in R.glutinosa and lays a foundation for future studies on the effects of epigenetics on the synthesis of secondary metabolites.

Study on DNA Methylation Status of WT1 Gene in Its Promoter Region in Hematologic Neoplasm Cell Lines.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 4386-4386
Author(s):  
Ye Zhao ◽  
Zi-xing Chen ◽  
Shao-yan Hu ◽  
Jian-nong Cen
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Cell Lines ◽  
Promoter Region ◽  
U937 Cell ◽  
Methylation Status ◽  
Gene Promoter ◽  
Epigenetic Mechanism ◽  
Wt1 Gene ◽  
Gene Promoter Region

Abstract The methylation at CpG island in the promoter region of a gene is one of the important epigenetic mechanism which regulates the gene activity. To study the DNA methylation pattern of WT1 gene promoter region within hematologic neoplastic cell lines and its correlation with WT1 gene expression by using the PCR-based methods. RT-PCR and Methylation-specific PCR were performed to study the WT1 gene expression in 8226, HL-60, Jurkat, K562, KG-1, NB4, Raji, SHI-1, U266 and U937 cell lines and the DNA methylation status in promoter region of WT1 gene. After treatment of U937 cell line by 5-aza-CdR, a demethylation inducing agent, the changes of WT1 gene expression level and the methylation status in its promter region in U937 cells was determined. Our Results showed that HL-60, K562, KG-1, NB4, SHI-1 cell lines demonstrated higher level of WT1 expression, while extremely low level was found in 8226, Jurkat, Raji, U266 and U937. The DNA hypermethylation in WT1 gene promoter region was identified in 8226, Jurkat, Raji, U266 and U937 cell lines. The WT1 gene expression in U937 was markedly enhanced after treatment with 5-aza-CdR in company with the decrease of methylated level and the increase of unmethylated level in its promoter region. These results indicate that modulation of the DNA methylation in WT1 promoter region is one of the epigenetic mechanisms to regulate its expression.

scholarly journals Genetic and Epigenetic Alterations Induced by Pesticide Exposure: Integrated Analysis of Gene Expression, microRNA Expression and DNA Methylation Datasets

2021 ◽  
Vol 18 (16) ◽  
pp. 8697
Author(s):  
Federica Giambò ◽  
Gian Leone ◽  
Giuseppe Gattuso ◽  
Roberta Rizzo ◽  
Alessia Cosentino ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Pesticide Exposure ◽  
Methylation Status ◽  
Microrna Expression ◽  
Integrated Analysis ◽  
Epigenetic Alterations ◽  
Expression Levels ◽  
Prediction Tools

Environmental or occupational exposure to pesticides is considered one of the main risk factors for the development of various diseases. Behind the development of pesticide-associated pathologies, there are both genetic and epigenetic alterations, where these latter are mainly represented by the alteration in the expression levels of microRNAs and by the change in the methylation status of the DNA. At present, no studies have comprehensively evaluated the genetic and epigenetic alterations induced by pesticides; therefore, the aim of the present study was to identify modifications in gene miRNA expression and DNA methylation useful for the prediction of pesticide exposure. For this purpose, an integrated analysis of gene expression, microRNA expression, and DNA methylation datasets obtained from the GEO DataSets database was performed to identify putative genes, microRNAs, and DNA methylation hotspots associated with pesticide exposure and responsible for the development of different diseases. In addition, DIANA-miRPath, STRING, and GO Panther prediction tools were used to establish the functional role of the putative biomarkers identified. The results obtained demonstrated that pesticides can modulate the expression levels of different genes and induce different epigenetic alterations in the expression levels of miRNAs and in the modulation of DNA methylation status.

Epigenetic Determinants of Pathogenesis and Resistance to Proteosome Inhibition in Mantle Cell Lymphoma.

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 3373-3373 ◽  
Author(s):  
Tobias Gellen ◽  
Pei-Yu Kuo ◽  
Rita Shaknovich ◽  
Maria E Figueroa ◽  
Ari Melnick ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Transcription Factor ◽  
Tumor Suppressor ◽  
Mantle Cell Lymphoma ◽  
Cell Lines ◽  
Tumor Suppressor Genes ◽  
Cell Lymphoma ◽  
Mantle Cell ◽  
Hypermethylated Genes

Abstract Mantle Cell Lymphoma (MCL) is an aggressive tumor accounting for 5% of non Hodgkin’s lymphomas(NHL). Given the poor clinical outcomes in this disease with current therapy, it is of great importance to better understand disease pathogenesis. Since aberrant epigenetic gene regulation is a hallmark of cancer, we hypothesized that an unbiased genome-wide DNA methylation study would identify genes involved in MCL pathogenesis. Moreover, we hypothesized that aberrantly silenced/hypermethylated genes responsible for drug sensitivity in MCL could be pharmacologically manipulated for maximizing clinical benefit. To address these questions, we examined the abundance of DNA methylation in 25,000 promoter fragments using the HELP (HPA II Enzyme Ligation mediated PCR amplification) assay in MCL cell lines. This study revealed s substantial heterogeneity in genomic methylation between cell lines, possibly reflective of underlying biologic diversity in this disease. However, MCL cell lines did display consistent aberrant methylation when compared to naïve B cells extracted from normal human tonsils. Remarkably, among the 102 genes with a methylation fold change in >3 and p<0.0001 the majority (100) were hypermethylated in MCL vs. normal B cells. Amongst these genes we identified five tumor suppressor genes implicated in the pathogenesis of other cancers: Protocadherin 8,Paternally expressed gene 3 (PEG3),Myeloid leukemia factor 1, Transcription Factor AP-2 gamma and Homeobox D8. Interestingly. PEG3 and Protocadherin 8 are both known to be silenced by hypermethylation at their gene promoters in gastric and breast cancer respectively. These genes may also possibly function as tumor suppressor genes in MCL pathogenesis and are excellent candidates for future functional studies. We then integrated methylation and gene expression data to identify loci that were both significantly methylated and suppressed in MCL. To identify the pathways and biological processes most relevant to our data set of methylated genes, we queried the Ingenuity Pathway Analysis (IPA) Knowledge base with the top 560 hypermethylated genes (>2 Standard Deviation) across all MCL cell lines. An unsupervised core analysis from the IPA knowledge base using our gene set revealed gene networks revolving around tumor suppressor TP53 and the NPM1 transcription factor in MCL cell lines. Locus specific confirmation by MassArray confirmed methylation of the distal portion of the TP53 promotor in the MCL cell lines. Recently, the proteosome inhibitor Bortezomib(BZM) has been shown to have specific activity in MCL, with single agent response rates ~40% in heavily pretreated patients. We wondered whether aberrant epigenetic programming might contribute to resistance to this agent and whether reversal of DNA methylation could overcome cellular mechanisms of resistance to Bortezomib. Therefore, to determine whether pharmacologic re-expression of genes could overcome bortezomib resistance, we treated MINO (a Bortezomib-refractory MCL cell line) with two low doses of Decitabine (0.1 uM and 1 uM) for 48 hours and sequentially with 15 nM of Bortezomib (IC50) for an additional 48 hours. Pretreatment of BZM-resistant MINO cells with Decitabine significantly (p<0.001) reduced cell viability as compared to control, suggesting that Decitabine can overcome BZM resistance in this refractory cell line. We are currently determining which genes contribute to this effect and validating these results in patient samples from a prospective trial of BZM+EPOCH. We predict that this will provide the basis for future trials individualizing BZM based therapy based on methylation and gene expression signatures in MCL.

scholarly journals Investigation of the Role of CpG Methylation in Epithelial Mesenchymal Transition Master Genes in a Chemoresistant Ovarian Cancer Cell line

2021 ◽  
Author(s):  
Yaman Alghamian ◽  
Chadi Soukkarieh ◽  
Abdul Qader Abbady ◽  
Hossam Murad
Keyword(s):  
Gene Expression ◽  
Ovarian Cancer ◽  
Dna Methylation ◽  
Cell Line ◽  
Cell Lines ◽  
Cancer Cell ◽  
Epithelial Mesenchymal Transition ◽  
Mesenchymal Transition ◽  
Master Genes

Abstract Ovarian cancer is one of the commonly diagnosed cancers among women. Chemoresistant is an essential reason for treatment failure and high mortality. Emerging evidence connects epithelial mesenchymal transition (EMT) like changes and acquisition of chemoresistance in cancer. DNA methylation influences cellular processes including EMT. Here, we investigate EMT like changes in cisplatin-resistant A2780 ovarian cancer cells (A2780cis), and we study the DNA methylation role in EMT master genes regulation. Cell viability assay was carried to test the sensitivity of A2780, and A2780cis human cancer cell lines to cisplatin compared to other cancer cell lines. Differential mRNA expression of EMT markers using qPCR was conducted to investigate EMT like changes. The role of CpGs methylation in gene expression regulation was investigated by 5-azacytidine (5-aza) treatment. DNA methylation changes in EMT genes were identified using Methylscreen assay between A2780 and A2780cis cells. A2780cis maintains its cisplatin tolerance ability and exhibits phenotypic changes congruent with EMT. Methylscreen assay and qPCR study revealed DNA hypermethylation in promoters of epithelial adhesion molecules CDH1 and EPCAM in A2780cis compared to the cisplatin-sensitive parental cells, these changes were concomitant with gene expression down-regulation. DNA hypomethylation associated with transcription up-regulation of the mesenchymal marker TWIST2 was observed in the resistant cells. Azacytidine treatment confirmed the DNA methylation role in the regulation of gene expression of CDH1, EPCAM and TWIST2 genes. A2780cis cell line undergoes EMT like changes, and EMT master genes are regulated by DNA methylation. A better perception of the molecular alterations which correlate with chemoresistance may lead to therapeutic benefits such as chemosensitivity restoration.

TMEM130 regulates cell migration through DNA methylation in nasopharyngeal carcinoma

2021 ◽  
pp. 1-9
Author(s):  
Hong Liu ◽  
Yong Zhang ◽  
Wenqiang Chen ◽  
Yan Zhang ◽  
Wen Zhang
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Cell Migration ◽  
Nasopharyngeal Carcinoma ◽  
Mrna Expression ◽  
Cell Lines ◽  
Methylation Level ◽  
Methylation Status ◽  
Transcriptional Expression ◽  
Migration Ability

BACKGROUND: Nasopharyngeal carcinoma (NPC), the common malignant head and neck cancer, is highly prevalent in southern China. The molecular mechanism underlying NPC tumorigenesis is unclear. We used 5-Aza-CdR, a DNA methyltransferase inhibitor, to treat NPC cell lines and discovered that the expression of TMEM130 changed significantly compared with the untreatment cells. This study aimed to identify the relationship between the DNA methylation status of TMEM130 and NPC, and to explore the function of TMEM130 in NPC cell migration. METHODS: qRT-PCR was performed to investigate the transcriptional expression of TMEM130 in NPC. Bisulfite sequencing PCR and 5-Aza-CdR treatment were used to detect the methylation level of the TMEM130 promoter. Gene Expression Omnibus (GEO) datasets were obtained to identifiy the methylation status and mRNA expression of TMEM130 in NPC and normal control tissues. Transwell and western blot analyses were used to detect cell migration ability after transfection of TMEM130/NC plasmids in NPC cells. RESULTS: The transcriptional expression of TMEM130 was decreased in NPC cell lines compared with in the NP69 cell line. TMEM130 promoter was significantly hyper methylated in three NPC cell lines (C666, CNE, and HONE) but hypo methylated in NP69 cells. The methylation level was higher in NPC than normal control tissues. Additionally, treatment of NPC cells with 5-Aza-CdR increased the TMEM130 mRNA expression level. Overexpression of TMEM130 in NPC cell lines suppressed cell migration ability and affected some epithelial-mesenchymal transition-associated gene expression. CONCLUSIONS: This study is the first to investigate the expression and function of TMEM130 in NPC. It was found that TMEM130 hyper methylation might contribute to NPC migration and this gene might act as a tumor suppressor gene. TMEM130 is a promising biomarker for NPC diagnosis.

scholarly journals Specific Glycosylation of Membrane Proteins in Epithelial Ovarian Cancer Cell Lines: Glycan Structures Reflect Gene Expression and DNA Methylation Status

2014 ◽  
Vol 13 (9) ◽  
pp. 2213-2232 ◽  
Author(s):  
Merrina Anugraham ◽  
Francis Jacob ◽  
Sheri Nixdorf ◽  
Arun Vijay Everest-Dass ◽  
Viola Heinzelmann-Schwarz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Ovarian Cancer ◽  
Dna Methylation ◽  
Membrane Proteins ◽  
Epithelial Ovarian Cancer ◽  
Cell Lines ◽  
Ovarian Cancer Cell ◽  
Methylation Status ◽  
Epithelial Ovarian Cancer Cell ◽  
Ovarian Cancer Cell Lines

DNA Methylation Inhibites ANXA1 Gene Expression in Nasopharyngeal Carcinoma Cell Lines*

2009 ◽  
Vol 36 (10) ◽  
pp. 1319-1326 ◽  
Author(s):  
Shuang-Xiang TAN ◽  
Rui-Cheng HU ◽  
Ai-Guo DAI ◽  
Cen-E TANG ◽  
Hong YI ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Nasopharyngeal Carcinoma ◽  
Cell Lines ◽  
Carcinoma Cell ◽  
Nasopharyngeal Carcinoma Cell ◽  
Carcinoma Cell Lines

scholarly journals Epigenetic Changes During Mechanically Induced Osteogenic Lineage Commitment

2015 ◽  
Vol 137 (2) ◽  
Author(s):  
Julia C. Chen ◽  
Mardonn Chua ◽  
Raymond B. Bellon ◽  
Christopher R. Jacobs
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Shear Stress ◽  
Fluid Shear Stress ◽  
Methylation Status ◽  
Lineage Commitment ◽  
Fluid Shear ◽  
Osteogenic Lineage ◽  
Osteogenic Markers ◽  
Heterochromatin Structure

Osteogenic lineage commitment is often evaluated by analyzing gene expression. However, many genes are transiently expressed during differentiation. The availability of genes for expression is influenced by epigenetic state, which affects the heterochromatin structure. DNA methylation, a form of epigenetic regulation, is stable and heritable. Therefore, analyzing methylation status may be less temporally dependent and more informative for evaluating lineage commitment. Here we analyzed the effect of mechanical stimulation on osteogenic differentiation by applying fluid shear stress for 24 hr to osteocytes and then applying the osteocyte-conditioned medium (CM) to progenitor cells. We analyzed gene expression and changes in DNA methylation after 24 hr of exposure to the CM using quantitative real-time polymerase chain reaction and bisulfite sequencing. With fluid shear stress stimulation, methylation decreased for both adipogenic and osteogenic markers, which typically increases availability of genes for expression. After only 24 hr of exposure to CM, we also observed increases in expression of later osteogenic markers that are typically observed to increase after seven days or more with biochemical induction. However, we observed a decrease or no change in early osteogenic markers and decreases in adipogenic gene expression. Treatment of a demethylating agent produced an increase in all genes. The results indicate that fluid shear stress stimulation rapidly promotes the availability of genes for expression, but also specifically increases gene expression of later osteogenic markers.

scholarly journals Stress Modifies the Expression of Glucocorticoid-Responsive Genes by Acting at Epigenetic Levels in the Rat Prefrontal Cortex: Modulatory Activity of Lurasidone

2021 ◽  
Vol 22 (12) ◽  
pp. 6197
Author(s):  
Paola Brivio ◽  
Giulia Sbrini ◽  
Letizia Tarantini ◽  
Chiara Parravicini ◽  
Piotr Gruca ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Chronic Stress ◽  
Chronic Mild Stress ◽  
Male Rats ◽  
Mild Stress ◽  
Experimental Conditions ◽  
Glucocorticoid Responsive Element ◽  
Responsive Element

Epigenetics is one of the mechanisms by which environmental factors can alter brain function and may contribute to central nervous system disorders. Alterations of DNA methylation and miRNA expression can induce long-lasting changes in neurobiological processes. Hence, we investigated the effect of chronic stress, by employing the chronic mild stress (CMS) and the chronic restraint stress protocol, in adult male rats, on the glucocorticoid receptor (GR) function. We focused on DNA methylation specifically in the proximity of the glucocorticoid responsive element (GRE) of the GR responsive genes Gadd45β, Sgk1, and Gilz and on selected miRNA targeting these genes. Moreover, we assessed the role of the antipsychotic lurasidone in modulating these alterations. Chronic stress downregulated Gadd45β and Gilz gene expression and lurasidone normalized the Gadd45β modification. At the epigenetic level, CMS induced hypermethylation of the GRE of Gadd45β gene, an effect prevented by lurasidone treatment. These stress-induced alterations were still present even after a period of rest from stress, indicating the enduring nature of such changes. However, the contribution of miRNA to the alterations in gene expression was moderate in our experimental conditions. Our results demonstrated that chronic stress mainly affects Gadd45β expression and methylation, effects that are prolonged over time, suggesting that stress leads to changes in DNA methylation that last also after the cessation of stress procedure, and that lurasidone is a modifier of such mechanisms.

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