【Abstract】 Objective To investigate the relationship between methylation of tumor suppressor gene and gastric cancer. Methods The literatures in recent years about the concept of methylation, its biological significance and the relationship between DNA methylation/demethylation and gastric cancer were reviewed. The effects of methylation of different tumor suppressor genes on gastric cancer were also analyzed. Results The effect of aberrant methylation on the development and the progression of gastric cancer was still unclear but it was supposed that the inactivation of genes related with cell cycle regulation, mitotic checkpoint, apoptosis, DNA mismatch repair, metastasis suppression and so on might be attributable to the aberrant methylation in gastric cancer. Conclusion Aberrant methylation of tumor suppressor genes plays an important role in the development and progression of gastric cancer. The status of methylation of tumor suppressor genes may be used as a useful molecule marker for diagnosis, assessing metastasis and evaluating prognosis, and demethylation could possibly be a new therapy for gastric cancer.
Retinoblastoma (RB) is a common intraocular tumor in children, often leading to blindness or disability, and its pathogenesis involves genetic and epigenetic regulation. Epigenetics regulates gene expression through mechanisms such as DNA methylation and histone modification without altering the DNA sequence, and the imbalance of its homeostasis is considered a crucial factor in the development and progression of RB. Therapeutic strategies targeting these abnormal modifications offer new potential treatment avenues for RB. Although current research has highlighted the importance of epigenetics in RB, the specific mechanisms of action, the relationship with genetic bases, and the development of targeted drugs remain largely unknown. Therefore, further in-depth research into the epigenetic mechanisms of RB is of great significance for elucidating its carcinogenic mechanisms, identifying effective therapeutic targets, and developing new drugs.
ObjectiveTo explore the effects and molecular mechanisms of histone methylase G9a inhibitor BIX-01294 on apoptosis in esophageal squamous cell carcinoma (ESCC).MethodsMTT assay and Colony-forming Units were adopted to determine the effects of BIX-01294 on the growth and proliferation of ESCC cell lines EC109 and KYSE150. Flow cytometry was used to analyze the apoptosis status of ESCC cells after the treatment of BIX-01294. The effects of BIX-01294 treatment on the expressions of G9a catalytic product H3K9me2, DNA double-strand break (DSB) markers, and apoptosis-related proteins were detected by Western blotting.ResultsBIX-01294 inhibited the growth of EC109 and KYSE150 cells in a dose-dependent manner (P<0.05), and BIX-01294 with the inhibitory concentration 50% (IC50) significantly inhibited the formation of colony (P<0.05). After 24 hours treatment of BIX-01294 (IC50), the apoptosis rate of EC109 cells increased from 11.5%±2.1% to 42.5%±5.4%, and KYSE150 cells from 7.5%±0.9% to 49.2%±5.2% (P<0.05). The expression level of the G9a catalytic product, H3K9me2, significantly decreased (P<0.05); while the expression of the DSB marker γH2AX was dramatically enhanced (P<0.05). We also found that the mitochondrial apoptosis pathway was activated and the expression levels of cleaved caspase3 and cleaved PARP were significantly elevated (P<0.05).ConclusionBIX-01294, the inhibitor of methyltransferase G9a, prompted apoptosis in ESCC cells by inducing DSB damage and activating mitochondrial apoptosis pathway.
Objective To identify the N6-methyladenosine (m6A)-related characteristic genes analyzed by gene clustering and immune cell infiltration in myocardial ischemia-reperfusion injury (MI/RI) after cardiopulmonary bypass through machine learning. Methods The differential genes associated with m6A methylation were screened by the dataset GSE132176 in GEO, the samples of the dataset were clustered based on the differential gene expression profile, and the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the differential genes of the m6A cluster after clustering were performed to determine the gene function of the m6A cluster. R software was used to determine the better models in machine learning of support vector machine (SVM) model and random forest (RF) model, which were used to screen m6A-related characteristic genes in MI/RI, and construct characteristic gene nomogram to predict the incidence of disease. R software was used to analyze the correlation between characteristic genes and immune cells, and the online website was used to build a characteristic gene regulatory network. Results In this dataset, a total of 5 m6A-related differential genes were screened, and the gene expression profiles were divided into two clusters for cluster analysis. The enrichment analysis of m6A clusters showed that these genes were mainly involved in regulating monocytes differentiation, response to lipopolysaccharides, response to bacteria-derived molecules, cellular response to decreased oxygen levels, DNA transcription factor binding, DNA-binding transcription activator activity, RNA polymerase Ⅱ specificity, NOD-like receptor signaling pathway, fluid shear stress and atherosclerosis, tumor necrosis factor signaling pathway, interleukin-17 signaling pathway. The RF model was determined by R software as the better model, which determined that METTL3, YTHDF1, RBM15B and METTL14 were characteristic genes of MI/RI, and mast cells, type 1 helper lymphocytes (Th1), type 17 helper lymphocytes (Th17), and macrophages were found to be associated with MI/RI after cardiopulmonary bypass in immune cell infiltration. Conclusion The four characteristic genes METTL3, YTHDF1, RBM15B and METTL14 are obtained by machine learning, while cluster analysis and immune cell infiltration analysis can better reveal the pathophysiological process of MI/RI.
ObjectiveTo summarize mechanism of DNA methylation and histone methylation in liver fibrosis.MethodThe literatures on the DNA methylation and histone methylation during the liver fibrosis were reviewed and analyzed.ResultsThe DNA methylation and histone methylation were the important components of epigenetics. The up-regulation or down-regulation of genes during the liver fibrosis leaded to the activation or inactivation of the subsequent pathways. For example, the PTEN, SEPT9, Smad7, etc. were hypermethylated and the expressions were decreased in the liver fibrosis. The Spp1 was hypomethylated and the expression was increased in the liver fibrosis.ConclusionsMethylation affects expression of genes by altering epigenetics of genes. Systematic and in-depth study of role and mechanism of methylation in liver diseases provides a new direction and locations for some target treatments for liver disease.
ObjectiveTo investigate the difference of DNA methylation before and after bariatric surgery.MethodThe relevant literatures of the research on the changes of DNA methylation level and gene expression regulation in blood and tissues before and after bariatric surgery were retrieved and reviewed.ResultsDNA methylation was an important method of epigenetic regulation in organisms and its role in bariatric surgery had been paid more and more attention in recent years. Existing studies had found that there were changes of DNA methylation in blood and tissues before and after bariatric surgery. The degree of methylation varies with different follow-up time after bariatric surgery and the same gene had different degrees of methylation in different tissues, and some even had the opposite results.ConclusionsDNA methylation levels before and after bariatric surgery are different in different tissues. And studies with larger sample size and longer follow-up time are needed, to further reveal relationship among DNA methylation, obesity, and bariatric surgery.
Objective To integrate the result of whole genome expression data and whole genome promoter CpG island methylation data, to screen the epigenetic modulated differentially expressed genes from transformed porcine bone marrow mesenchymal stem cells (BMSCs) after long-term cultivation. Methods Bone marrow from 6 landrace pigs, 3-month-old about 50 kg weight, was aspirated from the medullary cavity of the proximal tibia. The BMSCs were isolated, and purified by Ficoll density gradient centrifugation combined with adherent culture method. The transfor mation of BMSCs was tested by several methods including cell morphology observation, karyotype analysis, clone forming in soft agarose, serum requirement assay, and tumor forming in mice. The Agilent Pig 4x44k Gene Expression Microarray was used to investigate the differentially expressed mRNA. The methylated genes expression profile was performed using customized pig methylation chip. The gene expression and DNA methylation profiles were integrated to find out the epigenetic modulated differentially expressed genes, and to complete the bioinformatic analysis. Results BMSCs showed a change in appearance, from the initial spindle shape to a more flatted morphology then to small contact shape. After additional passages, BMSCs gradually acquired recovery of proliferating capacity and transformation properties such as anchorage-independent growth, chromosomal abnormality, and tumor formation in nude mice. The gene chip analysis demonstrated that 257 genes were upregulated and 315 genes were downregulated during long-term cultures as well as multiple signal pathways transduction involved, such as cell cycle, ECM-receptor interaction, focal adhesion, regulation of actin cytoskeleton, pathways in cancer, and P53. The analysis from methylation chip of coding genes suggested epigenetic regulation was involved in BMSCs spontaneous transformation and play a important role on it; 962 genes were hypermethylated and 1219 genes were hypomethylated, which were involved in the biological process of cellular metabolic, structure, and tumor generation. The combined analysis of genes regulated by methylation in the transformation process of BMSCs found that the methylation changes of the 35 genes were contrary to the direction of expression change (correlation coefficient r=–0.686, P=0.000); in which the methylation level of 21 genes promoter regions were increased while the gene expression decreased, and the methylation level of the 14 genes promoter regions decreased and the gene expression increased. At the same time, KEGG enrichment analysis revealed multiple genes regulated by methylation, involved in stem cell differentiation and multiple cell signaling pathways. Among the 14 down-regulated genes, many of them have the role of regulating the interaction of tumor and immunization, and the change of the methylation status of the CDKN3 promoter region may be closely related to the cell oncology. Conclusion The results deepen our understanding of the crucial role of coding genes methylation modification in BMSCs transformation, and may provide new approach to establish safe criteria for BMSCs clinical applications and transformation prevention.
ObjectiveTo observe the expression and transcription of MART-1 in human uveal melanoma cell lines 92-1, 92-2, Ocm3, Me1285, as well as the possible effect of methylation on its expression.MethodsThe cell lines 92-1, 92-2, Ocm3 and Mel285 were cultured routinely and tested for MART-1 expression at protein and mRNA level by FACS analysis, Western blot and RT-PCR respectively. Methylation status of the MART-1 promoter region in all the cell lines were checked by Southern blots of DNA digested with methylation sensitive restriction enzymes.ResultsAs observed in FACS analysis and Western blot, 92-1, 92-2 and Ocm3 were MART-1 positive cell lines while Me1285 was negative cell line. Consistent with protein analysis, 92-1 and Ocm3 cell lines showed MART-1 specific PCR products and there was no product in Me1285 cell line in RT-PCR. The MART-1 positive cell lines, 92-1, 92-2, and Ocm3 show methylation at the MspI/HpaⅡ site, and the NruⅠ sites of all positive cell lines are not methylated. The MART-1 negative cell line Mel285 shows hypermethylation at the NruⅠsite and the MspⅠ/HpaⅡ site is not methylated.ConclusionsMART-1 could be expressed in human uveal melanoma cell lines 92-1, 92-2 and Ocm3. The change of methylation status of MART-1 promoter may correlate with the transcription of MART-1.
Lung cancer is the most common malignant tumor in the world and the leading cause of cancer-related death. Due to the lack of effective early diagnosis methods, the prognosis of lung cancer is poor, but compared with advanced lung cancer, the survival rate of early lung cancer is greatly improved. Therefore, early diagnosis of lung cancer is crucial. As a major epigenetic modification, DNA methylation plays an important role in the development of lung cancer. A large number of studies have shown that detection of tumor suppressor gene methylation is an ideal early diagnosis method for lung cancer. With the continuous improvement of detection technology, methylation detection of multiple genes can be achieved. And it is found that multi-gene methylation combined detection of tissue samples obtained by minimally invasive operation such as puncture of diseased tissue and puncture of lymph node tissue, as well as the noninvasive samples such as peripheral blood, bronchoalveolar lavage fluid and sputum have higher detection rate and higher sensitivity and specificity than single gene methylation. It is an ideal method for early diagnosis of lung cancer.