Detection and Analysis of RNAs Expression Profile for Methylated Candidate Tumor Suppressor Genes in Nasopharyngeal Carcinoma

Background:DNA methylation, which acts as an expression regulator for multiple Tumor Suppressor Genes (TSGs), is believed to play an important role in Nasopharyngeal Carcinoma (NPC) development.Methods:We compared the effects of 5-aza-2-deoxycytidine (decitabine, DAC) on gene expression using RNA sequencing in NPC cells.Results:We analyzed Differentially Expressed Genes (DEGs) in NPC cells using DAC demethylation treatment and found that 2182 genes were significantly upregulated (≥ 2-fold change), suggesting that they may play a key role in cell growth, proliferation, development, and death. For data analysis, we used the Gene Ontology database and pathway enrichment analysis of the DEGs to discover differential patterns of DNA methylation associated with changes in gene expression. Furthermore, we evaluated 74 methylated candidate TSGs from the DEGs in NPC cells and summarized these genes in several important signaling pathways frequently disrupted by promoter methylation in NPC tumorigenesis.Conclusion:Our study analyzes the DEGs and identifies a set of genes whose promoter methylation in NPC cells is reversed by DAC. These genes are potential substrates of DNMT inhibitors and may serve as tumor suppressors in NPC cells.

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Promoter Methylation of Multiple Genes in Germinal Center Hyperplasia and Lymphomas of Germinal Center Origin

Blood ◽

10.1182/blood.v112.11.4487.4487 ◽

2008 ◽

Vol 112 (11) ◽

pp. 4487-4487

Author(s):

Jose M Paz-Carreira ◽

Raquel Losada ◽

Arantxa Garcia-Rivero ◽

Augusto Alvarez ◽

Fernando Bal ◽

...

Keyword(s):

Dna Methylation ◽

Tumor Suppressor ◽

B Cell ◽

Promoter Methylation ◽

Germinal Center ◽

Tumor Suppressor Genes ◽

Methylation Status ◽

Promoter Hypermethylation ◽

Epigenetic Mechanism ◽

Suppressor Genes

Abstract INTRODUCTION. Germinal centers (GC) are unique sites in peripheral lymphoid tissue where clonal selection of B cells takes place. This occurs as a response to stimulation by various antigens originating, sometimes, follicular hyperplasia (FH). GC have been known as a major source of B-cell lymphomas including follicular (FL) and diffuse large cell (DLCL). DNA methylation of tumor-suppressor genes is a mechanism of gene silencing involved in the pathogenesis of FL and DLCL. Much less is known about the role of methylation in FH. We determined the methylation status of 6 tumor-suppressor genes in 43 patients with FH, 18 patients with FL and 49 patients with DLCL in order to see the differential implication of this epigenetic mechanism in the pathological and the physiological development of GC. MATERIAL AND METHODS. Genomic DNA extracted from paraffin-embedded samples of 43 FH, 18 FL and 49 DLCL after being treated with EZ DNA-Methylation Kit (Zymo Research) with the manufacturer’s instructions, were analyzed by methylation-specific polymerase chain-reaction to determine promoter hypermethylation of DAP-k, SHP1, Rarβ, p14, SHP1, MGMT and PDRM1. All samples were obtained mostly from lymph nodes and tonsils. Diagnosis was based on morphology and immunohistochemistry analysis. All cases were matched for age, sex and ethnic origin. RESULTS: DAP-k promoter methylation occurred with higher frequency in FL(89%) than in DLCL(78%) and FH(40%). SHP1 was methylated in 61% of FL, 58% of FH and 23% of DLCL. RARb was methylated in 67% of FL patients, 30% of DLCL and only 12% of FH. Eight (44%) FL, seventeen (35%) DLCL and four (10%) BFH patients showed MGMT methylation. Promoter hypermethylation of p14 was detected only in 5 (12%) FH, 2 (4%) DLCL and none FL patients. Methylation of PRMD1 was present only in 1 (6%) FL, 2 (6%) DLCL and 1 (4%) FH samples. CONCLUSIONS. Inactivacion of DAP-K and SHP1 is present in B-cell malignancies, DLCL and FL, and BFH. Therefore, it may represent a physiologic event conferring a temporal survival advantage necessary for a GC hyperplastic response. Inactivation of the retinoic acid response through the methylation of Rarâ is significantly more frequent in lymphomas than in FH. As reported in other tumors methylation of MGMT is more frequent in lymphomas than in FH. With our data methylation of Cyclin dependent kinase inhibitors p14 is not a differential pathogenic event in lymphomas of GC origin, in fact it is more frequent in FH. Promoter Methylation of PDRM1 is not the mechanism involved in lymphomagenesis in FL and DLCL, the two FH positive deserve further follow-up to determine its significance.

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DNA methylation profiling in MEN1-related pancreatic neuroendocrine tumors reveals a potential epigenetic target for treatment

Acta Endocrinologica ◽

10.1530/eje-18-0195 ◽

2018 ◽

Vol 179 (3) ◽

pp. 153-160 ◽

Cited By ~ 5

Author(s):

E B Conemans ◽

L Lodewijk ◽

C B Moelans ◽

G J A Offerhaus ◽

C R C Pieterman ◽

...

Keyword(s):

Dna Methylation ◽

Tumor Suppressor ◽

Promoter Methylation ◽

Tumor Suppressor Genes ◽

Gene Promoter ◽

Pancreatic Neuroendocrine Tumor ◽

Promoter Hypermethylation ◽

Suppressor Gene ◽

Suppressor Genes ◽

Frequent Event

ObjectiveEpigenetic changes contribute to pancreatic neuroendocrine tumor (PanNET) development. Hypermethylation of promoter DNA as a cause of tumor suppressor gene silencing is a well-established oncogenic mechanism that is potentially reversible and therefore an interesting therapeutic target. Multiple endocrine neoplasia type 1 (MEN1) is the most frequent cause of inherited PanNETs. The aim of this study was to determine promoter methylation profiles in MEN1-related PanNETs.Design and methodsMethylation-specific multiplex ligation-dependent probe amplification was used to assess promoter methylation of 56 tumor suppressor genes in MEN1-related (n = 61) and sporadic (n = 34) PanNETs. Differences in cumulative methylation index (CMI), individual methylation percentages and frequency of promoter hypermethylation between subgroups were analyzed.ResultsWe found promoter methylation of a large number of potential tumor suppressor genes. CMI (median CMI: 912 vs 876,P = 0.207) was the same in MEN1-related and sporadic PanNETs. We found higher methylation percentages ofCASP8in MEN1-related PanNETs (median: 59% vs 16.5%,P = 0.002). In MEN1-related non-functioning PanNETs, the CMI was higher in larger PanNETs (>2 cm) (median: 969.5 vs 838.5;P = 0.021) and in PanNETs with liver metastases (median: 1036 vs 869;P = 0.013). Hypermethylation ofMGMT2was more frequent in non-functioning PanNETs compared to insulinomas (median: 44.7% vs 8.3%;P = 0.022). Hypermethylation of the Von Hippel–Lindau gene promoter was observed in one MEN1-related PanNET and was associated with loss of protein expression.ConclusionPromoter hypermethylation is a frequent event in MEN1-related and sporadic PanNETs. Targeting DNA methylation could be of therapeutic value in MEN1 patients with advanced PanNETs.

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Consistent DNA Hypermethylation Patterns in Laryngeal Papillomas

International Journal of Head and Neck Surgery ◽

10.5005/jp-journals-10001-1013 ◽

2010 ◽

Vol 1 (2) ◽

pp. 69-77 ◽

Cited By ~ 8

Author(s):

Josena K Stephen ◽

Kang Mei Chen ◽

Veena Shah ◽

Vanessa G Schweitzer ◽

Glendon Gardner ◽

...

Keyword(s):

Dna Methylation ◽

Tumor Suppressor ◽

Tumor Suppressor Genes ◽

Methylation Status ◽

Promoter Hypermethylation ◽

Aberrant Methylation ◽

Dna Hypermethylation ◽

Suppressor Genes ◽

Multiple Tumor ◽

Specific Pcr

Abstract Introduction This study examined the contribution of promoter hypermethylation to the pathogenesis of respiratory papillomatosis (RP), including recurrences (RRP) and progression to squamous cell carcinoma (SSC). Materials and methods A retrospective cohort of 25 laryngeal papilloma cases included 21 RRP, two of which progressed to SCC. Aberrant methylation status was determined using the multigene (22 tumor suppressor genes) methylation-specific multiplex ligationdependent probe amplification assay and confirmed using methylation specific PCR. Results Twenty genes had altered DNA methylation in 22 of 25 cases. Aberrant methylation of CDKN2B and TIMP3 was most frequent. Promoter hypermethylation of BRCA2, APC, CDKN2A and CDKN2B was detected in 2 RRP cases with subsequent progression to SCC. Of the 25 cases, 22 were positive for HPV-6, 2 for HPV-11 and 1 for HPV-16 and 33. Conclusion Consistent aberrant methylation of multiple tumor suppressor genes contributes to the pathogenesis of laryngeal papillomas. Persistent aberrant DNA methylation events in 2 RRP cases that progressed to cancer indicate an epigenetic monoclonal progression continuum to SCC.

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Abnormal promoter methylation of multiple tumor suppressor genes in human bronchial epithelial malignant cells

Biomedical Reports ◽

10.3892/br.2014.268 ◽

2014 ◽

Vol 2 (4) ◽

pp. 525-528 ◽

Cited By ~ 4

Author(s):

CHAOYANG LIU ◽

PENG LI ◽

DEWEI GAO ◽

PINGKUN ZHOU ◽

YUN SHAO ◽

...

Keyword(s):

Tumor Suppressor ◽

Promoter Methylation ◽

Tumor Suppressor Genes ◽

Malignant Cells ◽

Suppressor Genes ◽

Bronchial Epithelial ◽

Multiple Tumor

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Efficacy of decitabine in malignant meningioma cells: relation to promoter demethylation of distinct tumor suppressor and oncogenes and independence from TERT

Journal of Neurosurgery ◽

10.3171/2020.7.jns193097 ◽

2020 ◽

pp. 1-10

Author(s):

Louise Stögbauer ◽

Christian Thomas ◽

Andrea Wagner ◽

Nils Warneke ◽

Eva Christine Bunk ◽

...

Keyword(s):

Dna Methylation ◽

Tumor Suppressor ◽

Promoter Methylation ◽

Tumor Suppressor Genes ◽

Telomerase Activity ◽

High Grade ◽

Htert Promoter ◽

Men 1 ◽

Meningioma Cell ◽

Tert Expression

OBJECTIVEChemotherapeutic options for meningiomas refractory to surgery or irradiation are largely unknown. Human telomerase reverse transcriptase (hTERT) promoter methylation with subsequent TERT expression and telomerase activity, key features in oncogenesis, are found in most high-grade meningiomas. Therefore, the authors investigated the impact of the demethylating agent decitabine (5-aza-2ʹ-deoxycytidine) on survival and DNA methylation in meningioma cells.METHODShTERT promoter methylation, telomerase activity, TERT expression, and cell viability and proliferation were investigated prior to and after incubation with decitabine in two benign (HBL-52 and Ben-Men 1) and one malignant (IOMM-Lee) meningioma cell line. The global effects of decitabine on DNA methylation were additionally explored with DNA methylation profiling.RESULTSHigh levels of TERT expression, telomerase activity, and hTERT promoter methylation were found in IOMM-Lee and Ben-Men 1 but not in HBL-52 cells. Decitabine induced a dose-dependent significant decrease of proliferation and viability after incubation with doses from 1 to 10 μM in IOMM-Lee but not in HBL-52 or Ben-Men 1 cells. However, effects in IOMM-Lee cells were not related to TERT expression, telomerase activity, or hTERT promoter methylation. Genome-wide methylation analyses revealed distinct demethylation of 14 DNA regions after drug administration in the decitabine-sensitive IOMM-Lee but not in the decitabine-resistant HBL-52 cells. Differentially methylated regions covered promoter regions of 11 genes, including several oncogenes and tumor suppressor genes that to the authors’ knowledge have not yet been described in meningiomas.CONCLUSIONSDecitabine decreases proliferation and viability in high-grade but not in benign meningioma cell lines. The effects of decitabine are TERT independent but related to DNA methylation changes of promoters of distinct tumor suppressor genes and oncogenes.

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Association Between Cyclin D1 Polymorphism with CpG Island Promoter Methylation Status of Tumor Suppressor Genes in Gastric Cancer

Digestive Diseases and Sciences ◽

10.1007/s10620-010-1206-5 ◽

2010 ◽

Vol 55 (12) ◽

pp. 3449-3457 ◽

Cited By ~ 3

Author(s):

Tomomitsu Tahara ◽

Tomoyuki Shibata ◽

Masakatsu Nakamura ◽

Hiromi Yamashita ◽

Daisuke Yoshioka ◽

...

Keyword(s):

Gastric Cancer ◽

Tumor Suppressor ◽

Cyclin D1 ◽

Promoter Methylation ◽

Tumor Suppressor Genes ◽

Cpg Island ◽

Methylation Status ◽

Suppressor Genes ◽

Promoter Methylation Status

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Multiple steps in carcinogenesis involving alterations of multiple tumor suppressor genes

The FASEB Journal ◽

10.1096/fasebj.7.10.8344488 ◽

1993 ◽

Vol 7 (10) ◽

pp. 920-925 ◽

Cited By ~ 65

Author(s):

Jun Yokota ◽

Takashi Sugimura

Keyword(s):

Tumor Suppressor ◽

Tumor Suppressor Genes ◽

Suppressor Genes ◽

Multiple Tumor

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Targeting DNA methylation for treating triple-negative breast cancer

Pharmacogenomics ◽

10.2217/pgs-2019-0078 ◽

2019 ◽

Vol 20 (16) ◽

pp. 1151-1157 ◽

Cited By ~ 3

Author(s):

Jia Yu ◽

Jacqueline Zayas ◽

Bo Qin ◽

Liewei Wang

Keyword(s):

Breast Cancer ◽

Dna Methylation ◽

Tumor Suppressor ◽

Triple Negative Breast Cancer ◽

Targeted Therapies ◽

Tumor Suppressor Genes ◽

Dna Methyltransferase ◽

Triple Negative ◽

Suppressor Genes ◽

Dna Methyltransferase Inhibitors

Triple-negative breast cancer (TNBC) accounts for 15–20% of all invasive breast cancers and tends to have aggressive histological features and poor clinical outcomes. Unlike, estrogen receptor- or HER2-positive diseases, TNBC patients currently lack the US FDA-approved targeted therapies. DNA methylation is a critical mechanism of epigenetic modification. It is well known that aberrant DNA methylation contributes to the malignant transformation of cells by silencing critical tumor suppressor genes. DNA methyltransferase inhibitors reactivate silenced tumor suppressor genes and result in tumor growth arrest, with therapeutic effects observed in patients with hematologic malignancies. The antitumor effect of these DNA methyltransferase inhibitors has also been explored in solid tumors, especially in TNBC that currently lacks targeted therapies.

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