scholarly journals Pervasive promoter hypermethylation of silenced TERT alleles in human cancers

2020 ◽  
Vol 43 (5) ◽  
pp. 847-861 ◽  
Author(s):  
David Esopi ◽  
Mindy Kim Graham ◽  
Jacqueline A. Brosnan-Cashman ◽  
Jennifer Meyers ◽  
Ajay Vaghasia ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cancer Cells ◽  
Cell Lines ◽  
Cancer Cell ◽  
Transcriptional Repression ◽  
Cpg Island ◽  
Promoter Hypermethylation ◽  
Fine Tuning ◽  
Open Chromatin ◽  
Promoter Mutations

Abstract Background In cancers, maintenance of telomeres often occurs through activation of the catalytic subunit of telomerase, encoded by TERT. Yet, most cancers show only modest levels of TERT gene expression, even in the context of activating hotspot promoter mutations (C228T and C250T). The role of epigenetic mechanisms, including DNA methylation, in regulating TERT gene expression in cancer cells is as yet not fully understood. Methods Here, we have carried out the most comprehensive characterization to date of TERT promoter methylation using ultra-deep bisulfite sequencing spanning the CpG island surrounding the core TERT promoter in 96 different human cell lines, including primary, immortalized and cancer cell types, as well as in control and reference samples. Results In general, we observed that immortalized and cancer cell lines were hypermethylated in a region upstream of the recurrent C228T and C250T TERT promoter mutations, while non-malignant primary cells were comparatively hypomethylated in this region. However, at the allele-level, we generally found that hypermethylation of promoter sequences in cancer cells is associated with repressed expression, and the remaining unmethylated alleles marked with open chromatin are largely responsible for the observed TERT expression in cancer cells. Conclusions Our findings suggest that hypermethylation of the TERT promoter alleles signals transcriptional repression of those alleles, leading to attenuation of TERT activation in cancer cells. This type of fine tuning of TERT expression may account for the modest activation of TERT expression in most cancers.

scholarly journals Pervasive promoter hypermethylation of silenced TERT alleles in human cancers

2020 ◽  
Author(s):  
D Esopi ◽  
MK Graham ◽  
J Brosnan-Cashman ◽  
J Meyers ◽  
A Vaghasia ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cancer Cells ◽  
Cell Lines ◽  
Transcriptional Repression ◽  
Cpg Island ◽  
Promoter Hypermethylation ◽  
Open Chromatin ◽  
Promoter Sequences ◽  
Promoter Mutations

ABSTRACTIn cancers, maintenance of telomeres often occurs through activation of the catalytic subunit of telomerase, encoded by TERT. Yet, most cancers show only modest levels of telomerase gene expression, even in the context of activating hotspot promoter mutations (C228T and C250T). The role of epigenetic mechanisms, including DNA methylation, in regulating telomerase gene expression in cancer cells is not fully understood. Here, we have carried out the most comprehensive characterization to date of TERT promoter methylation using ultra-deep bisulfite sequencing spanning the CpG island surrounding the core TERT promoter in 96 different human cell lines. In general, we observed that immortalized and cancer cell lines were hypermethylated in a region upstream of the recurrent C228T and C250T TERT promoter mutations, while non-malignant primary cells were comparatively hypomethylated in this region. However, at the allele-level, we generally observe hypermethylation of promoter sequences in cancer cells is associated with repressed expression, and the remaining unmethylated alleles marked with open chromatin are largely responsible for the observed TERT expression in cancer cells. Our findings suggest that hypermethylation of the TERT promoter alleles signals transcriptional repression of those alleles, leading to the attenuation of TERT activation in cancer cells.SIGNIFICANCEHypermethylation of the TERT promoter alleles to attenuate TERT activation in cancer cells may account for the modest activation of TERT expression in most cancers.

scholarly journals ADAMTS1, CRABP1, and NR3C1 Identified as Epigenetically Deregulated Genes in Colorectal Tumorigenesis

2006 ◽  
Vol 28 (5-6) ◽  
pp. 259-272 ◽  
Author(s):  
Guro E. Lind ◽  
Kristine Kleivi ◽  
Gunn I. Meling ◽  
Manuel R. Teixeira ◽  
Espen Thiis-Evensen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Colon Cancer ◽  
Cell Lines ◽  
Cancer Cell ◽  
Cpg Island ◽  
Promoter Hypermethylation ◽  
Cancer Cell Lines ◽  
Colon Cancer Cell ◽  
Colorectal Carcinomas ◽  
Colon Cancer Cell Lines

Background: Gene silencing through CpG island hypermethylation is a major mechanism in cancer development. In the present study, we aimed to identify and validate novel target genes inactivated through promoter hypermethylation in colorectal tumor development. Methods: With the use of microarrays, the gene expression profiles of colon cancer cell lines before and after treatment with the demethylating agent 5-aza-2′-deoxycytidine were identified and compared. The expression of the responding genes was compared with microarray expression data of primary colorectal carcinomas. Four of these down-regulated genes were subjected to methylation-specific PCR, bisulphite sequencing, and quantitative gene expression analysis using tumors (n=198), normal tissues (n=44), and cell lines (n=30). Results: Twenty-one genes with a CpG island in their promoter responded to treatment in cell lines, and were simultaneously down-regulated in primary colorectal carcinomas. Among 20 colon cancer cell lines, hypermethylation was subsequently identified for three of four analyzed genes, ADAMTS1 (85%), CRABP1 (90%), and NR3C1 (35%). For the latter two genes, hypermethylation was significantly associated with absence or reduced gene expression. The methylation status of ADAMTS1, CRABP1, and NR3C1 was further investigated in 116 colorectal carcinomas and adenomas. Twenty-three of 63 (37%), 7/60 (12%), and 2/63 (3%) adenomas, as well as 37/52 (71%), 25/51 (49%), and 13/51 (25%) carcinomas were hypermethylated for the respective genes. These genes were unmethylated in tumors (n=82) from three other organs, prostate, testis, and kidney. Finally, analysis of normal colorectal mucosa demonstrated that the observed promoter hypermethylation was cancer-specific. Conclusion: By using a refined microarray screening approach we present three genes with cancer-specific hypermethylation in colorectal tumors, ADAMTS1, CRABP1, and NR3C1.

Determining the Relative Gene Expression Level of Hypoxia Related Genes in Different Cancer Cell Lines

2020 ◽  
Vol 14 (1) ◽  
pp. 52-59
Author(s):  
Laila Baqlouq ◽  
Malek Zihlif ◽  
Hana Hammad ◽  
Tuqa M. Abu Thaib
Keyword(s):  
Gene Expression ◽  
Cancer Cells ◽  
Cell Line ◽  
Cell Lines ◽  
Cancer Cell ◽  
Cancer Cell Lines ◽  
Breast Epithelial Cell ◽  
Pcr Array ◽  
Pancreatic Cancer Cells ◽  
Inducible Genes

Objective: This study aims to identify the changes in expression of hypoxia-inducible genes in seven different cancer cell lines that vary in their oxygen levels in an attempt to identify hypoxia biomarkers that can be targeted in therapy. Profiling of hypoxia inducible-gene expression of these different cancer cell lines can be used as a baseline data for further studies. Methods: Human cancer cell lines obtained from the American Type Culture Collection were used; MCF7 breast cancer cells, PANC1 pancreatic cancer cells, PC-3 prostate cancer cells, SH-SY5Y neuroblastoma brain cancer cells, A549 lung cancer cells, and HEPG2 hepatocellular carcinoma. In addition, we used MCF10A non-tumorigenic human breast epithelial cell line as a normal cell line. The differences in gene expression were examined using real-time PCR array (PAHS-032Z, Human Hypoxia Signaling Pathway PCR Array) and analyzed using the ΔΔCt method. Results: Almost all hypoxia-inducible genes showed a PO2-dependent up- and down-regulated expression. Noticeable gene expression differences were identified. The most important changes occurred in the HIF1α and NF-KB signaling pathways targeted genes and in central carbon metabolism pathway genes such as HKs, PFKL, and solute transporters. Conclusion: This study identified possible hypoxia biomarkers genes such as NF-KB, HIF1α, HK, PFKL, and PIM1 that were expressed in all hypoxic cells. Pleotropic pathways that play a role in inducing hypoxia directly such as HIF1 α and NF-kB pathways were upregulated. In addition, genes expressed only in the severe hypoxic liver and pancreatic cells indicate that severe and intermediate hypoxic cancer cells vary in their gene expression. Gene expression differences between cancer and normal cells showed the shift in gene expression profile to survive and proliferate under hypoxia.

Oncolytic adenovirus expressing apoptotic genes targets radiation resistant (RR) esophageal cancer

2007 ◽  
Vol 25 (18_suppl) ◽  
pp. 21043-21043
Author(s):  
J. Y. Chang ◽  
R. Komaki ◽  
X. Zhang ◽  
L. Wang ◽  
B. Fang
Keyword(s):  
Gene Expression ◽  
Esophageal Cancer ◽  
Radiation Exposure ◽  
Cancer Cells ◽  
Cell Lines ◽  
Cancer Cell ◽  
Esophageal Cancer Cell ◽  
Esophageal Cancer Cells ◽  
Trans Gene ◽  
Fractionated Radiation

21043 Background: Only 25% of esophageal cancer patients achieve pathological complete response after standard chemoradiotherapy. Radiation dose escalation is associated with higher toxicity but no therapeutic improvement. In addition, esophageal cancer cells may develop radiation resistance (RR) after fractionated radiation exposure. Therefore, molecular targeting therapy for RR esophageal cancer is urgently needed. Methods: Six pairs of RR esophageal cancer cell lines were established by applying continuous 2 Gy fractionated irradiation. Ad/TRAIL-E1, an oncolytic adenoviral vector expressing both apoptotic TRAIL and viral E1A genes under the control of tumor specific human telomerase reverse transcriptase promoter, was constructed. Phosphate buffer solution and vectors expressing the TRAIL gene only, the GFP marker protein only, or the E1A gene only served as controls. Trans-gene expression, apoptosis activation, and the RR esophageal cancer cells targeted were evaluated in vitro and in vivo. A human esophageal RR cancer model was established and locally treated with Ad/TRAIL-E1 or controls. Results: After fractionated radiation exposure, esophageal cancer cell lines developed RR (up to 25-fold) that was associated with activation of the anti-apoptotic pathway. Ad/TRAIL-E1 activated an apoptotic cascade of caspases and selectively killed esophageal cancer cells but not normal cells. Ad/TRAIL-E1 preferentially targeted RR stem-like cancer cells with higher trans-gene expression and cell killing compared with parental cells. Overexpression (3 times) of Coxsackie's and adenoviral receptors in RR esophageal cancer cells compared with parental cells was noted. Ad/TRAIL-E1 therapy resulted in 40% tumor-free survival without the treatment- related toxicity found in human RR esophageal adenocarcinoma mouse models (p<0.05 as compared with controls). Conclusions: Esophageal cancer cells develop RR after fractionated radiation exposure. Ad/TRAIL-E1 preferentially targeted RR stem-like esophageal cancer cells, which resulted in a 40% cure rate. No significant financial relationships to disclose.

Genomic editing of intronic enhancers unveils their role in fine-tuning tissue-specific gene expression in Arabidopsis thaliana

2021 ◽  
Author(s):  
Fanli Meng ◽  
Hainan Zhao ◽  
Bo Zhu ◽  
Tao Zhang ◽  
Mingyu Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Transcriptional Repression ◽  
Regulation Of Gene Expression ◽  
Fine Tuning ◽  
Specific Gene ◽  
Open Chromatin ◽  
Floral Tissue ◽  
Deletion Lines ◽  
A Genome

Abstract Enhancers located in introns are abundant and play a major role in the regulation of gene expression in mammalian species. By contrast, the functions of intronic enhancers in plants have largely been unexplored and only a handful of plant intronic enhancers have been reported. We performed a genome-wide prediction of intronic enhancers in Arabidopsis thaliana using open chromatin signatures based on DNase I sequencing. We identified 941 candidate intronic enhancers associated with 806 genes in seedling tissue and 1,271 intronic enhancers associated with 1,069 genes in floral tissue. We validated the function of 15 of 21 (71%) of the predicted intronic enhancers in transgenic assays using a reporter gene. We also created deletion lines of three intronic enhancers associated with two different genes using CRISPR/Cas. Deletion of these enhancers, which span key transcription factor binding sites, did not abolish gene expression but caused varying levels of transcriptional repression of their cognate genes. Remarkably, the transcriptional repression of the deletion lines occurred at specific developmental stages and resulted in distinct phenotypic effects on plant morphology and development. Clearly, these three intronic enhancers are important in fine-tuning tissue- and development-specific expression of their cognate genes.

scholarly journals MMP1 and MMP11 expression in Peripheral Blood Mononuclear Cells upon their interaction with Breast Cancer Cells and Fibroblasts

2020 ◽  
Author(s):  
Noemi Eiro ◽  
Sandra Cid ◽  
Nuria Aguado ◽  
María Fraile ◽  
Jorge Rubén Cabrera ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Cancer Cells ◽  
Cancer Patients ◽  
Cell Lines ◽  
Cancer Cell ◽  
Breast Cancer Cell ◽  
Breast Cancer Cell Lines ◽  
Breast Cancer Patients ◽  
Inflammatory Genes

Abstract Background: Tumor-infiltrating immune cells phenotype is associated with tumor progression. However, little is known about the phenotype of the Peripheral Blood Mononuclear Cells (PBMC) from breast cancer patients. Here, we investigated the expression of MMP1 and MMP11 in PBMC from breast cancer patients and we analyzed gene expression changes upon their interaction with cancer cells and Cancer-Associated Fibroblasts (CAF). Finally, we measured the impact of PBMC in proinflammatory genes expression in normal fibroblast and CAF.Results: Gene expression of MMP1 and MMP11 in PBMC from breast cancer patients (n=54) and control (n=28), and expression of IL1A, IL6, IL17, IFNβ and NFB in breast cancer cell lines (MCF-7 and MDA-MB-231), CAF and in Normal Fibroblasts (NF) were analyzed by qRT-PCR before and after co-culture. Our results show the existence of a group of breast cancer patients (25.9%) with very high levels of MMP11 gene expression in PBMC. Also, we present evidence of increased gene expression of MMP1 and MMP11 in PBMC after co-culture with breast cancer cell lines, NF or CAF. Finally, we show a differential expression profile of inflammatory genes in NF and CAF when co-cultured with control or breast cancer PBMC.Conclusions: We have observed that MMPs expression in PBMC is regulated by the microenvironment, while the expression of inflammatory genes in NF or CAF is differentially regulated by control or breast cancer PBMC. These findings confirm the importance of the interaction and communication between stromal cells and suggest that PBMC would play a role to promote an aggressive tumor behavior.

scholarly journals Eryngium Billardieri Induces Apoptosis via Bax Gene Expression in Pancreatic Cancer Cells

2018 ◽  
Vol 8 (4) ◽  
pp. 667-674 ◽  
Author(s):  
Neda Roshanravan ◽  
Parina Asgharian ◽  
Hassan Dariushnejad ◽  
Naimeh Mesri Alamdari ◽  
Behzad Mansoori ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pancreatic Cancer ◽  
Flow Cytometry ◽  
Cyclin D1 ◽  
Cancer Cells ◽  
Cell Lines ◽  
Cancer Cell ◽  
Mtt Assay ◽  
Cancer Cell Lines ◽  
Therapeutic Effects

Purpose: Pancreatic adenocarcinoma has a high prevalence all over the world. Most of the therapeutic approaches failed as a result of tumor invasion and rapid metastasis. Several natural plants have been shown to have promising therapeutic effects. Thus, the aim of this study was to investigate the cytotoxic activity of Eryngium billardieri against PANC-1 cancer cell lines. Methods: Dimethylthiazole diphenyltetrazolium bromide assay (MTT assay) and flow cytometry were used to assess the cytotoxicity of E. billardieri extracts against PANC-1 cancer cell lines. Quantitative Polymerase Chain Reaction (qPCR) was conducted to investigate the expression levels of Bcl2- associated X protein (BAX) and cyclin D1. Results: The results of the MTT assay showed that E. billardieri extracts had cytotoxic effects on PANC- 1 cancer cell lines. Moreover, the findings from the gene expression confirmed the over expression of Bax, and under expression of cyclin D1 following treatment with dichloromethane (DCM) and n-hexane (n- hex) extracts in cancer cells (P < 0.05). Interestingly, the flow cytometry results showed that DCM and n- hex extracts of E. billardieri induced apoptosis in PANC- 1 cancer cell lines. Conclusion: The results of this study demonstrated that DCM and n- hex extracts of E. billardieri significantly induce apoptosis by increasing Bax and decreasing cyclin D1 mRNA expression. Therefore, E. billardieri may be regarded as a novel approach for treatment of pancreatic cancer as a result of its promising apoptotic and cytotoxic properties.

scholarly journals Promoter hypermethylation downregulates RUNX3 gene expression in colorectal cancer cell lines

Oncogene ◽  
2004 ◽  
Vol 23 (40) ◽  
pp. 6736-6742 ◽  
Author(s):  
Ja-Lok Ku ◽  
Sung-Bum Kang ◽  
Young-Kyoung Shin ◽  
Hio Chung Kang ◽  
Sung-Hye Hong ◽  
...  
Keyword(s):  
Gene Expression ◽  
Colorectal Cancer ◽  
Cell Lines ◽  
Cancer Cell ◽  
Promoter Hypermethylation ◽  
Cancer Cell Lines ◽  
Colorectal Cancer Cell ◽  
Colorectal Cancer Cell Lines ◽  
Runx3 Gene

scholarly journals Transcriptome Remodeling in Gradual Development of Inverse Resistance between Paclitaxel and Cisplatin in Ovarian Cancer Cells

2020 ◽  
Vol 21 (23) ◽  
pp. 9218
Author(s):  
Jolanta Szenajch ◽  
Alicja Szabelska-Beręsewicz ◽  
Aleksandra Świercz ◽  
Joanna Zyprych-Walczak ◽  
Idzi Siatkowski ◽  
...  
Keyword(s):  
Gene Expression ◽  
Ovarian Cancer ◽  
Cancer Cells ◽  
Cell Lines ◽  
Cancer Cell ◽  
Ovarian Cancer Cell ◽  
Cancer Cell Lines ◽  
Ovarian Cancer Cells ◽  
Resistance Development ◽  
Receptor Family

Resistance to anti-cancer drugs is the main challenge in oncology. In pre-clinical studies, established cancer cell lines are primary tools in deciphering molecular mechanisms of this phenomenon. In this study, we proposed a new, transcriptome-focused approach, utilizing a model of isogenic cancer cell lines with gradually changing resistance. We analyzed trends in gene expression in the aim to find out a scaffold of resistance development process. The ovarian cancer cell line A2780 was treated with stepwise increased concentrations of paclitaxel (PTX) to generate a series of drug resistant sublines. To monitor transcriptome changes we submitted them to mRNA-sequencing, followed by the identification of differentially expressed genes (DEGs), principal component analysis (PCA), and hierarchical clustering. Functional interactions of proteins, encoded by DEGs, were analyzed by building protein-protein interaction (PPI) networks. We obtained human ovarian cancer cell lines with gradually developed resistance to PTX and collateral sensitivity to cisplatin (CDDP) (inverse resistance). In their transcriptomes, we identified two groups of DEGs: (1) With fluctuations in expression in the course of resistance acquiring; and (2) with a consistently changed expression at each stage of resistance development, constituting a scaffold of the process. In the scaffold PPI network, the cell cycle regulator—polo-like kinase 2 (PLK2); proteins belonging to the tumor necrosis factor (TNF) ligand and receptor family, as well as to the ephrin receptor family were found, and moreover, proteins linked to osteo- and chondrogenesis and the nervous system development. Our cellular model of drug resistance allowed for keeping track of trends in gene expression and studying this phenomenon as a process of evolution, reflected by global transcriptome remodeling. This approach enabled us to explore novel candidate genes and surmise that abrogation of the osteomimic phenotype in ovarian cancer cells might occur during the development of inverse resistance between PTX and CDDP.

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