Objective To investigate the possible mechanism of arsenic trioxide (As2O3) inducing P16 gene demethylation and transcription regulation in the retinoblastoma (RB) Cell Line Y79． Methods The induced growth inhibition of Y79 cell was assayed by MTT; The DNA content of Y79 cell was analyzed by flow cytometry after being exposed to As2O3; the methylation status of the P16 gene in Y79 cell line before and after treatment with As2O3 was detected by the nestedmethylation specific PCR and DNA sequencing; the mRNA of P16,DNA methyltransferases (DNMT3A and 3B)gene were determined by RT-PCR． Results As2O3 was able to inhibit the growth of Y79 cell and increase the cell number in G0-G1 phase；P16 gene was not expressed in Y79 cell line and As2O3 can induce itrsquo;s mRNA expression；after 48 hour disposal of As2O3，the methylation levelof P16 gene was apparently attenuated in Y79 cell line,the expression of DNMT3A and DNMT3B was obviously down-regulated． Conclusions P16 gene is the hypermethylation in the retinoblastoma cell line Y79, and As2O3 can inhibite the methylation of P16 gene and upregulate the expression of p16 gene mRNA which inhibits the proliferation of Y79 cell by inducing the G0-G1 arrest, by inhibiting the expression of DNA methyltransferases.
Objective To investigate the expression of the histone deacetylases 1( HDAC1) and the level of whole histone acetylation and methylation in lung T cells of asthmatic rats, and investigate their role in the pathogenesis of asthma.Methods Sixteen wistar rats were randomly divided into a control group and an asthma group( n =8 in each group) . The rats was sensitized with ovalbumin( OVA) and challenged with aerosol OVA to establish asthma model. The asthmatic ratmodel was confirmed by measurement of pulmonary function, histochemical staining, HE staining, and the levels of interleukin-4 ( IL-4 ) , interferon-gamma ( IFN-γ) and immunoglobulin E( IgE) in serum and bronchoalveolar lavage fluid ( BALF) . T cells were isolated fromrat lungs and the purity was identified. The expression of the HDAC1, the level of whole histone H3 and H4 acetylation, and whole H3K9 dimethylation were analyzed by Western blot in lung T cells. Results Compared with the control group, the protein expression of HDAC1 was significantly lower( 0. 465±0. 087 vs 0. 790 ±0. 076, P lt;0. 05) in lung T cells of the asthma group. No significant differences werefound in regard to the level of whole histone H3 and H4 acetylation and whole H3K9 dimethylation betweenthe two groups. Conclusions HDAC1 in lung T cells may be involved in the pathogenesis of asthma.Histone modification by HDAC1 may be a specific eventwith gene transcription which may not be associated with asthma.
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 explore the accuracy of machine learning algorithms based on SHOX2 and RASSF1A methylation levels in predicting early-stage lung adenocarcinoma pathological types. MethodsA retrospective analysis was conducted on formalin-fixed paraffin-embedded (FFPE) specimens from patients who underwent lung tumor resection surgery at Affiliated Hospital of Nantong University from January 2021 to January 2023. Based on the pathological classification of the tumors, patients were divided into three groups: a benign tumor/adenocarcinoma in situ (BT/AIS) group, a minimally invasive adenocarcinoma (MIA) group, and an invasive adenocarcinoma (IA) group. The methylation levels of SHOX2 and RASSF1A in FFPE specimens were measured using the LungMe kit through methylation-specific PCR (MS-PCR). Using the methylation levels of SHOX2 and RASSF1A as predictive variables, various machine learning algorithms (including logistic regression, XGBoost, random forest, and naive Bayes) were employed to predict different lung adenocarcinoma pathological types. ResultsA total of 272 patients were included. The average ages of patients in the BT/AIS, MIA, and IA groups were 57.97, 61.31, and 63.84 years, respectively. The proportions of female patients were 55.38%, 61.11%, and 61.36%, respectively. In the early-stage lung adenocarcinoma prediction model established based on SHOX2 and RASSF1A methylation levels, the random forest and XGBoost models performed well in predicting each pathological type. The C-statistics of the random forest model for the BT/AIS, MIA, and IA groups were 0.71, 0.72, and 0.78, respectively. The C-statistics of the XGBoost model for the BT/AIS, MIA, and IA groups were 0.70, 0.75, and 0.77, respectively. The naive Bayes model only showed robust performance in the IA group, with a C-statistic of 0.73, indicating some predictive ability. The logistic regression model performed the worst among all groups, showing no predictive ability for any group. Through decision curve analysis, the random forest model demonstrated higher net benefit in predicting BT/AIS and MIA pathological types, indicating its potential value in clinical application. ConclusionMachine learning algorithms based on SHOX2 and RASSF1A methylation levels have high accuracy in predicting early-stage lung adenocarcinoma pathological types.
ObjectiveRecent advancements in the researches on cholangiocarcinoma (CC) related genes methylation in CC were reviewed and the clinical significances of aberrant DNA methylation for the diagnosis and treatment of CC were discussed. MethodsRelevant literatures about the relation between CC-related genes methylation and CC published recently were collected and reviewed. ResultsThe genesis of CC resulted from abnormal expressions of many genes. Many researches had shown that the abnormal methylation of CC-related genes had a close relation with CC. Epigenetic alteration had been acknowledged as an important mechanism contributing to early CC carcinogenesis. ConclusionsAbnormal methylation of CC-related genes is related with CC. The detection of CC-related genes methylation might provide new specific biomarkers for early noninvasive diagnosis of this disease. Using epigenetic agents such as azacytidine to modulate the activities of DNA methyltransferase and reverse the methylation status of CC-related gene might be an attractive strategy for future treatment of CC, which could be combined with conventional therapies.
ObjectiveTo determine the level of CDH1 gene promoter hypermethylation in human gastric carcinoma by establishing MS-PCR method, and analyze retrospectively the possible statistical relationship between CDH1 gene promoter hypermethylation in human gastric carcinoma and HP infection, tumor differentiation, invasion, lymph nodal and distant metastasis, respectively. MethodsThe bisulfite conversion MS-PCR method was adopted to examine the level of CDH1 gene promoter hypermethylation in 40 cases of human gastric carcinoma tissue collected between January 2008 and December 2009. The statistical relationship between CDH1 gene promoter hypermethylation in human gastric carcinoma and HP infection, tumor differentiation, invasion, lymph nodal and distant metastasis were examined respectively with SPSS statistical tools. ResultsThe positive rate of CDH1 gene promoter hypermethylation in gastric carcinomas (67.5%) was higher than that in paired normal gastric mucosae (12.5%), and the difference was significant (P<0.05). In gastric carcinomas, the positive rate of CDH1 gene promoter hypermethylation in well differentiated or moderately differentiated groups (22.2%) was lower than that in poorly differentiated groups (80.6%), and the difference was significant (P<0.05). The positive rate of CDH1 gene promoter hypermethylation in HP positive groups (78.1%) was higher than that in HP negative groups (25.0%), and the difference was significant (P<0.05). ConclusionCDH1 gene promoter hypermethylation may play an important role in the process of tumor carcinogenesis in gastric carcinomas. Meanwhile, the CDH1 gene promoter hypermethylation may lead to poor differentiation in gastric carcinomas. CDH1 gene promoter hypermethylation is related to HP infection in the original gastric carcinomas, which shows that HP may get involved in the process of tumor suppressor gene methylation/inactivation and tumor development process.
ObjectiveTo evaluate the clinical value of a combined diagnostic model integrating circulating cell-free DNA (cfDNA) methylation markers and CT imaging features for differentiating benign and malignant lung nodules and for early lung cancer detection. This study pioneers a two-step multi-omics modeling approach to construct a robust diagnostic model. MethodsA retrospective cohort of 140 patients (70 malignant and 70 benign, confirmed by postoperative pathology) with lung nodules who underwent surgical treatment at West China Hospital, Sichuan University, from January 2014 to December 2024 was included. Methylation profiles of 54 cfDNA regions were detected via targeted methylation sequencing. CT imaging features (e.g., nodule size, type, and signs) were extracted. A two-step modeling strategy was applied: ① imaging features were modeled directly using binary logistic regression, while methylation features were selected via LASSO regression before modeling; ② a combined model was constructed using the scores from both models. Model performance was evaluated using receiver operating characteristic (ROC) curves, with internal validation via Bootstrap (1000 iterations). ResultsAll patients were split into a training set (n=84) and a test set (n=56). In the test set, the combined model achieved an area under the ROC curve (AUC) of 0.86 [95% confidence interval (CI): 0.74-0.95], with both sensitivity and specificity reaching 82%. This outperformed the individual imaging model (AUC=0.74) and methylation model (AUC=0.82). ConclusionThe multi-omics combined diagnostic model significantly improved the ability to distinguish benign from malignant lung nodules, particularly for early-stage lesions like ground-glass opacities. Its non-invasive and high-sensitivity features provide a promising translational tool for lung cancer screening, with promising clinical application prospects.
ObjectiveTo systematically review the effectiveness and safety of demethylation agents in patients with myelodysplastic syndrome. MethodsRandomized controlled trials (RCTs) about demethylation agents in treating myelodysplastic syndrome was electronically searched in PubMed, EMbase, The Cochrane Library (Issue 3, 2013), Web of Science, CNKI, VIP, WanFang Data and CBM from inception to March 2013. Two reviewers independently screened literature according to the inclusion and exclusion criteria, extracted data, and assessed methodological quality of the included studies. Meta-analysis was performed using RevMan 5.1 software. ResultsA total of 4 studies involving 816 patients were finally included. The results of meta-analysis showed that:for patients with myelodysplastic syndrome at middle/advanced stage, compared with the best supportive treatment plan, demethylation agents improved complete remission (CR) (OR=19.14, 95%CI 5.33 to 68.7, P < 0.000 01), partial remission (PR) (OR=20.63, 95%CI 5.76 to 73.93, P < 0.000 01), hematological improvement (HI) (OR=3.58, 95%CI 2.40 to 5.34, P < 0.000 01), and the incidences of Grade Ⅲ or Ⅳ neutropenia (OR=3.82, 95%CI 2.67 to 5.47, P < 0.000 01), Grade Ⅲ or Ⅳ thrombocytopenia (OR=3.98, 95%CI 2.55 to 6.23, P < 0.000 01), and mortalities (OR=0.52, 95%CI 0.35 to 0.77, P < 0.000 01), all with significant differences; and part of patients suffered from Grade Ⅲ or Ⅳ thrombocytopenia and tolerable adverse reaction caused by non-hematologic change. ConclusionCurrent evidence suggests that demethylation agents in treating myelodysplastic syndrome have apparently curative effects. Besides, it could prolong the time of turning into acute myelocytic leukemia, reduce mortalities, and improve patients' quality of life.
Objective To investigate the role of DNA methylation on regulation of cell apoptosis and proliferation in ischemia-reperfusion of small intestine. Methods Thirty-five male Wistar rats were randomly divided into normal group， sham operation group， and ischemia-reperfusion group. The apoptotic cell was assessed by TUNEL and electron microscopy and the expression of Ki-67 was examined by immunohistochemistry in the small intestinal parts （villi epithe-lium， crypt epithelium， and lamina propria mucosa of small intestine）. The DNA methylation was detected by DNA histo-endonuclease-linked detection of methylated DNA sites. Results ①The apoptotic positive cells increased at 3 h， 6 h，and 12 h after ischemia-reperfusion in the villi epithelium， crypt epithelium， and lamina propria mucosa of small intestine as compared with the normal group and sham operation group （P＜0.01）；Moreover， the apoptotic cells in the lamina propria mucosa of small intestine were identified as T cells by electron microscopy. ②The expressions of Ki-67 markedly increased at 3 h， 6 h， 12 h， and 24 h after ischemia-reperfusion in the villi epithelium cells as compared with the normal group and sham operation group （P＜0.01）. ③The weak expression of DNA methylation was found in the villi epith-elium and crypt epithelium in the normal group and sham operation group， the b expression was examined in the crypt epithelium cells nearby stem cell site in the ischemia-reperfusion of small intestine， the change of expression was gradually weak from crypt epithelium to villi epithelium. Conclusion This initial results indicate that the DNA methyl-ation in the ischemia-reperfusion of small intestine might regulate cell apoptosis and proliferation.
ObjectiveTo explore the role of DNA methylation in the pathogenesis of cholangiocarcinoma and its progress as a therapeutic target for cholangiocarcinoma.MethodThe relevant literatures at home and abroad in recent years about the DNA methylation and cholangiocarcinoma were reviewed.ResultsMethylation is a frequent event in cholangiocarcinoma and effect the occurrence and development of cholangiocarcinogenesis. DNA methylation inhibitors reactivate tumor suppressor genes.ConclusionsDNA methylation is closely related to the cholangiocarcinogenesis. Despite there is no effective clinical therapeutics and diagnosis at present, with further study, DNA methylation is expected to be one of the new target to treatment and diagnosis this disease.