DNA methylation status of hMLH1, p16INK4a, and CDH1 is not associated with mRNA expression levels of DNA methyltransferase and DNA demethylase in gastric carcinomas

Abstract Abstract 4645 DNA hypermethylation has been implicated in the tumorigenesis and prognosis in acute myeloid leukemia (AML). To identify and validate relevant methylated genes in AML, we have compared expression levels and methylation status of 26 candidate genes. One of the interesting candidates identified in our study is MSX2. MSX2 is a member of muscle segment homeobox gene family. MSX2 plays a role in promoting cell growth under certain conditions and may be an important target for RAS signaling pathways. However, the mechanism of transcriptional regulation and functional role of MSX2 in hematological malignancies, especially AML, are poorly understood. In our study, we determined the methylation status, and analyzed the expression levels of MSX2 in AML cell lines and primary AML cells using RT-PCR and/or Taqman real-time PCR. MSX2 mRNA expression was robust in the normal granulocytes and blasts of human bone-marrow, but was either absent or significantly diminished in 6 of 9 (66.7%) AML cell lines. The expression levels of MSX2 in those 6 AML cell lines were restored after treatment of 5-aza 2′-deoxycytidine. In addition, COBRA (Combined Bisulfite Restriction) analysis demonstrated hypermethylation of MSX2 in those AML cell lines (6 of 9, 66.7%), and partial methylation in 3 of 9 AML cell lines. The methylation status was inversely correlated with the mRNA expression levels of MSX2 in those cell lines. Furthermore, the expression levels and methylation status of MSX2 in human primary AML cells were evaluated. COBRA analysis demonstrated frequent hypermethylation of MSX2 in primary AML patient samples (19 of 32, 59.3%). Importantly, the mRNA expression levels of MSX2 as shown by Taqman real-time PCR in those 19 primary AML patient samples were inversely correlated with the methylation status of MSX2. These findings confirmed the role of frequent DNA hypermethylation in silencing MSX2 in AML. We are in the process of determining the functional role of MSX2 in the pathogenesis of AML. In addition, diagnostic and prognostic values of MSX2 in AML are being pursued. Disclosures: No relevant conflicts of interest to declare.

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Differences in Expression Patterns of DNMTs and TSG Proteins in Lymphoid Tissue Section Play an Important Role in Their Association

Blood ◽

10.1182/blood.v126.23.2657.2657 ◽

2015 ◽

Vol 126 (23) ◽

pp. 2657-2657

Author(s):

Lobna Alkebsi ◽

Hiroshi Handa ◽

Kenichi Tahara ◽

Hiroaki Shimizu ◽

Takuma Ishizaki ◽

...

Keyword(s):

B Cells ◽

Protein Expression ◽

Mrna Expression ◽

Lymphoid Tissue ◽

Methylation Status ◽

Lymphoid Tissues ◽

Expression Levels ◽

Protein Expressions ◽

Mrna Expression Levels ◽

E Cadherin

Abstract In situ, patterns of expression of DNMTs (DNA methytransferases) in normal reactive tonsillar tissue have been examined. Difference in pattering of expression of DNMTs and TSG (Tumor suppressor genes) proteins in lymphoid tissue section is an important question in relation to their association with each other as well as relationship to mRNA gene expression level. In order to examine this issue, we examined DNMTs and TSG proteins expression by immunohistochemistry in sections of paraffin-embedded specimens obtained from 33 subjects of lymphoma and 16 subjects of Non-malignant tissues after receiving written informed consent. The specimens were stained with anti-DNMTs (DNMT1, DNMT3A and DNMT3B) and anti-TSG (E-cadherin, H-cadherin and ADAMTS18) antibodies. In addition, using fresh-frozen optimal cutting temperature (OCT) compound-embedded tissue specimens before any treatment, we examined mRNA expression levels and promoter methylation status of E-cadherin (CDH1), H-cadherin (CDH13) and a disintegrin and metalloproteinase with thrombospondin motifs (ADAMTS18) using quantitative real-time PCR (qRT-PCR) and methylation-specific PCR (MSP), respectively. The expression of nuclear DNMTs proteins (DNMT1 and 3A) in lymphoma section was observed in [17/33 (51%); 27/33 (81%)], whereas in non-malignant tissues was [14/16 (87.5%); 13/16 (81%)], respectively. The DNMT3B protein expression was not detected in our tissue samples, which might be explained by the fact that DNMT3B characterized by alternative splicing as shown previously. Membrane proteins (E-cadherin, H-cadherin and ADAMTS18) showed low expression [12/33 (36%); 10/33 (30%); 6/33 (18%), respectively], when compared to non-malignant tissue sections [12/16 (75%); 7/16 (43%); 8/16 (50%), respectively]. The expression levels of CDH1, CDH13 and ADAMTS18 mRNAs were non-significantly reduced in their corresponding protein negative expression compared to the levels in cases with positive protein expression (p =0.112, p =0.378, p =0.077, respectively). We could not find any correlation between mRNA/protein expression levels of DNMTs and the methylation status of CDH1, CDH13 and ADAMTS18. Importantly, by immunostaining especially in non-malignant lymphoid tissues, we found that DNMT1 was highly detected in germinal center B cells (GC B cells) with gradual decrease or no expression in the mantle, marginal, interfollicular and T cells zones. Whereas DNMT3A was preferentially and scattered like expressed in the cells of the surrounding zones out of the germinal centers. Furthermore, E-cadherin, H-cadherin and ADAMTS18 proteins expression were detected on the cell surface membrane of the cells outside the GC but at rates somehow more than those cells inside the GC (Fig. 1). This is supported by the significant association observed between the frequency of DNMT3A with both E-cadherin and ADAMTS18, protein expressions (Chi square: p <0.05), while no association with H-cadherin protein expression. In addition, DNMT1 protein expression did not show significant association with the protein expressions of E-cadherin, H-cadherin and ADAMTS18. Moreover, the mRNA expression levels of DNMT3A and 3B showed high significant levels (p <0.05) in cases with negative protein expressions of both E-cadherin and ADAMTS18 when compared to cases with positive protein expressions (Fig. 2A and C). The DNMT1 mRNA expression level did not show any significant difference between the negative and positive protein expressions of E-cadherin, H-cadherin and ADAMTS18 (Fig. 2B). Furthermore, there was no significant association between the mRNA levels of DNMTs and H-cadherin protein expression. Expression of H-cadherin protein was frequently observed in the endothelial venules and trabeculae of the lymphoid tissues (Fig. 1) which might cause of its lack of association with both DNMT1 and DNMT3A. In conclusion, these results indicate that as a result of differences in pattering of DNMTs and TSG protein expressions detected in lymphoid tissues by immunohistochemistry staining, it might be one of the reasons of the association with each other and their mRNA expression levels across the spectrum of lymphomas and non-malignant lymphoid tissues. Disclosures No relevant conflicts of interest to declare.

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The Promoter Methylation Status and mRNA Expression Levels ofCTCFandSIRT6in Sporadic Breast Cancer

DNA and Cell Biology ◽

10.1089/dna.2013.2257 ◽

2014 ◽

Vol 33 (9) ◽

pp. 581-590 ◽

Cited By ~ 9

Author(s):

Da Wang ◽

Changlong Li ◽

Xuemei Zhang

Keyword(s):

Breast Cancer ◽

Mrna Expression ◽

Promoter Methylation ◽

Sporadic Breast Cancer ◽

Methylation Status ◽

Expression Levels ◽

Promoter Methylation Status ◽

Mrna Expression Levels

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2′-Deoxy-5-Azacytidine Enhances Cytotoxic Effect Of Other Anti-Leukemic Agents Synergistically In Acute Lymphoblastic Leukemia Cell Line

Blood ◽

10.1182/blood.v122.21.5564.5564 ◽

2013 ◽

Vol 122 (21) ◽

pp. 5564-5564

Author(s):

Kimiyoshi Sakaguchi ◽

Hiroyoshi Takahashi

Keyword(s):

Mrna Expression ◽

Mtt Assay ◽

Research Funding ◽

Caspase 3 ◽

Lymphoblastic Leukemia ◽

Methylation Status ◽

Expression Levels ◽

Apoptotic Genes ◽

Mrna Expression Levels

Abstract Introduction Advances in chemotherapy have improved the outcome of childhood acute lymphoblastic leukemia (ALL). However, leukemia cells in refractory ALL are often resistant to anti-leukemic agents. Although recent studies have focused on the epigenetic changes in refractory leukemia, the relationship between the demethylating agent 2′-deoxy-5-azacytidine (decitabine, DAC) and ALL remains unclear. Here, we examine the combined effects of DAC and anti-leukemic agents such as clofarabine (CLO) and etoposide (ETO) on the ALL cell line CCRF-CEM. Methods and results In vitro drug sensitivity was measured using 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyl tetrazolium bromide (MTT) assay. We cultured CCRF-CEM cells for 72 hours with or without DAC, and then removed DAC (when present) prior to culturing CCRF-CEM cells for 48 hours with ETO or CLO, or without chemotherapeutic drugs. After culturing for 48 hours, we removed the chemotherapeutic drugs and measured in vitro drug sensitivity using MTT assay. The MTT assay was performed in triplicate. We then evaluated the inhibitory concentration at 50% (IC50). IC50 for ETO, ETO+DAC, CLO, and CLO+DAC was 3.36, 0.625, 4.96, and 1.92, respectively. The combination Index (CI) was produced with Calcusyn® software, which uses the methodology of Chou and Talalay to perform formal synergy analyses. A CI < 1 indicated a synergistic effect. The CI was 0.026 for ETO+DAC and 0.431 for CLO+DAC. We assayed with Annexin-V, PI staining, and caspase-3/7 to detect apoptosis. We observed apoptosis rates of 31.6%, 53.3%, 31.2%, and 52.6% for ETO, ETO+DAC, CLO, and CLO+DAC, respectively. We observed greater caspase-3/7 activity with DAC+CLO and DAC+ETO than with CLO and ETO. Using real-time reverse transcription polymerase chain reaction (RT-qPCR) in CCRF-CEM cells, we examined mRNA expression levels for the pro-apoptotic genes BAK, BID, BAX, BAD, BIM, PUMA, ATM, TP53, and NOXA, as well as those for the anti-apoptotic genes BCL2, BCL2L1, and XIAP. The expression level of each target gene was calculated by normalizing it to the housekeeping gene GAPDH. The RT-qPCR was performed in triplicate. We used Student’s t test to compare the data. We observed DAC increased mRNA expression levels of BAX and NOXA, but decreased those for BAK, BID, PUMA, BCL2L1, ATM, TP53, and XIAP. We then analyzed the methylation status of pro- and anti-apoptotic genes after 48 hours incubation with or without DAC. Methylation status of BAK, NOXA, BCL2L1 and XIAP incubation with DAC was 1.3%, 3.3%, 2.5% and 72.9%, respectively. Methylation status of BAK, NOXA, BCL2L1 and XIAP incubation without DAC was 1.9%, 3.6%, 0.7% and 92.3%, respectively. There was no significant difference. Discussion Our results showed that DAC synergistically enhances CLO and ETO cytotoxicity, and this cytotoxic effect depends on caspase-3/7 activity. We examined mRNA expression levels of pro- and anti-apoptotic genes. We hypothesized that DAC would increase mRNA expression levels of most pro-apoptotic genes, and decrease mRNA levels of most anti-apoptotic genes. We found that DAC decreased some pro-apoptotic genes, such as BAK, BID, PUMA, ATM, and TP53, which disproves our hypothesis. Our present findings are similar to those of Shin et al., who reported that DAC decreased BID mRNA expression levels. However, they provided no explanation for this activity. Our results show that DAC did not demethylate the CpG of BAK, NOXA, BCL2L1, or XIAP. Thus, DAC must demethylate the CpG of other genes. Nevertheless, many genes are involved in apoptosis, and it remains unclear which genes are demethylated by DAC. Disclosures: Sakaguchi: Yakult Honsha Company: Research Funding; Japan Leukemia Research Fund: Research Funding; Japan Society for the Promotion of Science: Research Funding; Sanofi: Research Funding; Teijin Pharma: Research Funding.

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Beta-defensins and analogs in Helicobacter pylori infections: mRNA expression levels, DNA methylation, and antibacterial activity

PLoS ONE ◽

10.1371/journal.pone.0222295 ◽

2019 ◽

Vol 14 (9) ◽

pp. e0222295 ◽

Cited By ~ 7

Author(s):

Raffaela Pero ◽

Tiziana Angrisano ◽

Mariarita Brancaccio ◽

Annarita Falanga ◽

Lucia Lombardi ◽

...

Keyword(s):

Dna Methylation ◽

Helicobacter Pylori ◽

Antibacterial Activity ◽

Mrna Expression ◽

Expression Levels ◽

Beta Defensins ◽

Mrna Expression Levels

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Effects of Melatonin on Prenatal Dexamethasone-Induced Epigenetic Alterations in Hippocampal Morphology and Reelin and Glutamic Acid Decarboxylase 67 Levels

Developmental Neuroscience ◽

10.1159/000368768 ◽

2015 ◽

Vol 37 (2) ◽

pp. 105-114 ◽

Cited By ~ 17

Author(s):

Chun-Chung Lui ◽

Mei-Hsin Hsu ◽

Ho-Chang Kuo ◽

Chih-Cheng Chen ◽

Jiunn-Ming Sheen ◽

...

Keyword(s):

Spatial Memory ◽

Glutamic Acid ◽

Mrna Expression ◽

Glutamic Acid Decarboxylase ◽

Dna Methyltransferase ◽

Brain Magnetic Resonance Imaging ◽

Acid Decarboxylase ◽

Expression Levels ◽

Hippocampal Morphology ◽

Mrna Expression Levels

Prenatal glucocorticoid exposure causes brain damage in adult offspring; however, the underlying mechanisms remain unclear. Melatonin has been shown to have beneficial effects in compromised pregnancies. Pregnant Sprague-Dawley rats were administered vehicle (VEH) or dexamethasone between gestation days 14 and 21. The programming effects of prenatal dexamethasone exposure on the brain were assessed at postnatal days (PND) 7, 42, and ∼120. Melatonin was administered from PND21 to the rats exposed to dexamethasone, and the outcome was assessed at ∼PND120. In total, there were four groups: VEH, vehicle plus melatonin (VEHM), prenatal dexamethasone-exposure (DEX), and prenatal dexamethasone exposure plus melatonin (DEXM). Spatial memory, gross hippocampal morphology, and hippocampal biochemistry were examined. Spatial memory assessed by the Morris water maze showed no significant differences among the four groups. Brain magnetic resonance imaging showed that all rats with prenatal dexamethasone exposure (DEX + DEXM) exhibited increased T2-weighted signals in the hippocampus. There were no significant differences in the levels of mRNA expression of hippocampal reln, which encodes reelin, and GAD1, which encodes glutamic acid decarboxylase 67, at PND7. At both PND42 and ∼PND120, reln and GAD1 mRNA expression levels were decreased. At ∼PND120, melatonin restored the reduced levels of hippocampal reln and GAD1 mRNA expression in the DEXM group. In addition, melatonin restored the reln mRNA expression levels by (1) reducing DNA methyltransferase 1 (DNMT1) mRNA expression and (2) reducing the binding of DNMT1 and the methyl-CpG binding protein 2 (MeCP2) to the reln promoter. The present study showed that prenatal dexamethasone exposure induced gross alterations in hippocampal morphology and reduced the levels of hippocampal mRNA expression of reln and GAD1. Spatial memory was unimpaired. Thus, melatonin had a beneficial effect in restoring hippocampal reln mRNA expression by reducing DNMT1 and MeCP2 binding to the reln promoter.

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Imprinting in the schizophrenia candidate gene GABRB2

European Psychiatry ◽

10.1016/s0924-9338(11)72528-7 ◽

2011 ◽

Vol 26 (S2) ◽

pp. 823-823

Author(s):

F. Pun ◽

C. Zhao ◽

W. Lo ◽

S. Ng ◽

S. Tsang ◽

...

Keyword(s):

Candidate Gene ◽

Mrna Expression ◽

Association Studies ◽

Methylation Status ◽

Dependent Manner ◽

Expression Levels ◽

Allele Specific ◽

Parent Of Origin ◽

Allele Specific Methylation ◽

Mrna Expression Levels

Imprinting, characterized by unequal expression of the offspring's genes in a parent-of-origin dependent manner, has been functionally implicated in brain development and in psychiatric disorders. In this study, unambiguous distortion in paternal but not maternal transmission of the disease-associated single-nucleotide polymorphism (SNP) rs6556547 (T/G) clearly indicated the presence of parent-of-origin effect (POE) in the GABAA receptor β2 subunit gene (GABRB2). ‘Flipping’ of allelic mRNA expression in heterozygotes of SNP rs2229944 (C/T) and the observed two-tiered distribution of mRNA expression levels in heterozygotes of the disease-associated SNP rs1816071 (G/A) furnished important support for the occurrence of imprinting at GABRB2. Imprinting in effect introduced heterozygotes from different parents-of-origin endowed with dissimilar mRNA expression capabilities. The deficit of upper-tiered expressions accounted for the lowered mRNA expression levels in the schizophrenic heterozygotes. This pointed to the necessity of differentiating between two kinds of heterozygotes of different parental origins in disease association studies on GABRB2. Bisulfite sequencing revealed hypermethylation in the neighborhood of SNP rs1816071, and methylation differences between controls and schizophrenia patients. Notably, allele-specific methylation was observed at the disease-associated SNPs rs6556547 and rs1816071. These findings raised the possibility that CpG methylation status of these sites could have an impact on the expression of GABRB2 and the risk of schizophrenia. Furthermore, the occurrence of imprinting and allele-specific methylation in the schizophrenia candidate gene GABRB2 was compatible with the epigenetic hypothesis for schizophrenia pathophysiology, thereby calling for the need to explore the role of epigenetic factors in mediating susceptibility to schizophrenia.

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DNA Methylation and SNPs of ABCA1 Gene Promoter Affect Gene Expression and Involve in the Pathological Mechanism of Ischemic Stroke

10.21203/rs.3.rs-998653/v1 ◽

2021 ◽

Author(s):

Zhihao Li ◽

Jun Wang ◽

Baixue Zhou ◽

Yang Liu ◽

Zhaojing Zhang ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Ischemic Stroke ◽

Mrna Expression ◽

Foam Cell ◽

Gene Promoter ◽

Control Group ◽

Expression Levels ◽

Pathological Mechanism ◽

Mrna Expression Levels

Abstract ATP binding cassette subfamily A1 (ABCA1) is a key protein in the formation of mature high density lipoprotein (HDL), which plays a crucial role in atherosclerosis. Accumulating evidence has shown that the expression levels of the ABCA1 gene are upregulated in ischemic stroke (IS) patients. However, the mechanism remains elusive. We hypothesized that DNA methylation and SNPs of ABCA1 gene promoter affect the expression levels of ABCA1 gene and involve in the pathological mechanism of IS. 100 patients with IS and 100 healthy controls were enrolled in the present study. Initially, the mRNA expression levels of ABCA1 gene were examined by qPCR and the methylation levels was detected by MethyTarget sequencing. Then, rs1800976, rs1800977, rs2246298, rs2437817, rs2740483, rs539621172 in promoter region of ABCA1 gene were selected for genotyping. Finally, the relationship between the methylation of ABCA1 gene and gene expression was verified by constructing THP-1 foam cell model. The mRNA expression levels of ABCA1 gene in the IS group were significantly higher than those in controls (P<0.05). 17 CpG sites in the promoter of ABCA1 gene were analyzed and the DNA methylation levels of CpG1, CpG7 and CpG15 sites in IS group was significantly lower than control group (P<0.05). Rs2740483, rs1800977 and rs2437817 were significantly correlated with CpG1. Rs1800977 was significantly correlated with CpG3. In summary, DNA methylation and rs2740483, rs1800977, rs2437817 of ABCA1 gene promoter affect the expression levels of ABCA1 gene, change the clearance rate of intracellular lipids, and participate in the pathogenesis of IS.

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XXYLT1 Methylation Contributes to the Occurrence of Lung Adenocarcinoma

10.21203/rs.2.22275/v1 ◽

2020 ◽

Author(s):

Hui Zeng ◽

ying wang ◽

yongjun zhang

Keyword(s):

Dna Methylation ◽

Lung Adenocarcinoma ◽

Mrna Expression ◽

Methylation Status ◽

Additional Research ◽

Expression Level ◽

Methylation Data ◽

Expression Levels ◽

Male Patients ◽

Cancer Tissues

Abstract Objective: This study aimed to observe the methylation levels and mRNA expression of XXYLT1 and to further analyze their possible correlation with the risk of lung adenocarcinoma. Methods: Thirty patients with lung adenocarcinoma (fifteen men and fifteen women) were recruited in this study. Cancer tissues and para-carcinoma tissues were obtained from each of the patients. The expression levels of XXYLT1 mRNA were determined, and the DNA methylation status was analyzed by MassARRAY Spectrometry. The methylation data of individual units were generated by EpiTyper v1.0.5 software. Results: Among the male patients, the expression level of XXYLT1 mRNA was significantly higher in the para-carcinoma tissues compared to the cancer tissues. Meanwhile, among the male patients, the methylation rates of three CpG units (CpG_23, CpG_25, and CpG_60.61.62.63.64.65) within the XXYLT1 gene were lower in the para-carcinoma tissues compared to the cancer tissues.Conclusions: Our results show that XXYLT1 mRNA was down-regulated and methylation rates were increased in lung adenocarcinoma tissues than in para-carcinoma tissues. These suggested that methylation of XXYLT1 may have significance in the pathogenesis of lung adenocarcinoma. Additional research is required to elucidate this aspect.

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