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 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.
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.
ObjectiveTo summarize the current research status of the relationship between DNA methylation and liver regeneration.MethodThe related literatures at home and abroad were searched to review the studies on relationships between the methylation level of liver cells, regulation of gene expression, and methylation related proteins and liver regeneration.ResultsThe DNA methylation was an important epigenetic regulation method in vivo and its role in the liver regeneration had been paid more and more attentions in recent years. The existing studies had found the epigenetic phenomena during the liver regeneration such as the genomic hypomethylation, methylation changes of related proliferating genes and DNA methyltransferase and UHRF1 regulation of the liver regeneration.ConclusionsThere are many relationships between DNA methylation and liver regeneration. Regulation of liver regeneration from DNA methylation level is expected to become a reality in the near future.
Objective To study the differential expression profiling of the transcripts modified by m5C methylation in a rat model of N-methyl-D-aspartate (NMDA)-induced retinal excitotoxicity. MethodsA total of 65 Sprague Dawley male rats aged 7-8 weeks were randomly divided into two groups: normal control group and NMDA group. The right eye (model eye) of rats in the NMDA group were injected with 50.0 mmol/L of NMDA 3 μl in the vitreous cavity, while in the normal control group, equal volume of normal saline was injected into the vitreous cavity. After 1 week of the injection, the optic nerve conduction function of rats was detected by visual evoked potential. The whole structure of rat retina was observed by hematoxylin-eosin staining, and the thickness of each retinal layer and the number of retinal ganglion cell layer were detected. The number of β3 tubulin immunofluorescence positive cells was detected by immunofluorescence staining on retinal stretched preparation. Total RNA was extracted from the retinas of normal control group and NMDA group, and high-throughput m5C modified RNA was sequenced, and bioinformatics analysis was performed. The relative expression levels of SLFN3, PLXNB3, CD36 and HIC2 mRNA in retina were detected by real-time quantitative polymerase chain reaction. The comparison between the two groups was performed using an unpaired t test. ResultsThe P1 latency of control group and NMDA group were (117.86±6.48) and (148.46±3.78) ms, and the amplitudes were (42.57±2.41) and (8.68±0.63) μV, respectively. Compared with the normal control group, the latency period was prolonged and the amplitude was significantly decreased in the NMDA group, with statistical significance (P＜0.001). In normal control group, retinal ganglion cells (RGC) were uniformly arranged with large round nuclei. In NMDA group, the volume of retinal RGC was atrophied and the number of RGC was reduced. The total retinal thickness in the control group and NMDA group was (207.51±12.76) μm and (187.51±12.54) μm, respectively. The number of β3 tubulin positive cells was 79.86±6.56 and 29.36±2.16, respectively. Compared with normal control group, the total retinal thickness and the number of β3 tubulin positive cells in NMDA group were decreased, with statistical significance (P＜0.001). Compared with the control group, 576 differentially expressed m5C mRNA were screened in the NMDA group, among which 230 up-regulated and 346 down-regulated genes were detected, respectively. The results of biological information analysis showed that compared with the control group, the upregulated m5C mRNA in the NMDA group was mainly involved in biological processes such as perception and cell-cell adhesion, and was mainly concentrated in the cytokine-cytokine receptor interaction and neural active ligand-receptor interaction pathway. The biological processes in which down-regulated m5C mRNA was mainly involved in biological processes such as G-protein-coupled receptor signaling pathway and cell communication, which were mainly concentrated in primary immune deficiency pathway and neural active ligand-receptor interaction pathway. Real-time quantitative polymerase chain reaction detection results showed that compared with the normal control group, the relative expression levels of SLFN3 and PLXNB3 mRNA in the retina of rats in NMDA group were significantly increased, while the relative expression levels of CD36 and HIC2 mRNA were significantly decreased, with statistical significance (P＜0.05). ConclusionIn NMDA induced retinal excitatory toxicity rat models, m5C modified retinal transcriptome showed abnormal expression.
ObjectiveTo explore the clinical significance of promoter hypermethylation of O6-methylguanine-DNA methyltransferase (MGMT) in cholangiocarcinoma. MethodsPromoter methylation status of MGMT gene and expression of MGMT protein were detected in cholangiocarcinoma by methylationspecific PCR and immunohistochemical staining, respectively. ResultsAberrant methylation of MGMT gene was detected in 17 patients (47.2%). Twentyone cases showed negative immunoreactivities. Of 21 patients with negative MGMT expression, 14 patients had aberrant methylation of MGMT gene. In 15 patients with positive MGMT expression, aberrant methylation of MGMT gene was only found in three cases. There was a negative correlation between promoter methylation status of MGMT gene and the expression of MGMT protein (rs=-0.816, Plt;0.05). Promoter methylation status of MGMT gene was related to depth of invasion, degree of differentiation, and TNM stage (Plt;0.05), but not to age of patient, gender, pathological type, and lymph node metastasis (Pgt;0.05). ConclusionsHypermethylation of MGMT promoter is a frequency molecular event in cholangiocarcinoma and may be involved in carcinogenesis. Methylation status of MGMT gene may be used to evaluate malignant degree of cholangiocarcinoma.
Objective To investigate the effects of DNA methyltransferase inhibitor (DNMTi) and histone deacetylase inhibitor (HDCAi) on expression of E-cadherin gene and invasiveness of cholangiocarcinoma cell. Methods According to different treatment, the QBC939 cells were divided into four groups: blank control group, hydralazine group, valproic acid group and hydralazine and valproic acid combined group. After 48 h, the expression of E-cadherin was evaluated by reverse transcription-PCR (RT-PCR), mehtylation specific PCR (MSP) and Western blot, the invasiveness of QBC939 cells was evaluated by Transwell method. Results There was no expression of E-cadherin mRNA and protien in blank control group and valproic acid group. The expressions of E-cadherin mRNA and protien in hydralazine and valproic acid combined group were higher than those in hydralazine group ( P ＜ 0.01), while the invasiveness of QBC939 cells of hydralazine and valproic acid combined group was much lower than that of blank control group, hydralazine group and valproic acid group ( P ＜ 0.01). Conclusion DNMTi and HDACi can synergistically re-express E-cadherin gene and weaken the invasiveness of QBC939 cell, which plays an important part in treatment of cholangiocarcinoma.
Objective To review the advance of gene diagnosis and gene therapy on gastric cancer. Methods Literatures about the advance of gene diagnosis and therapy on gastric cancer were reviewed. Results Detection of tumor marker by gene technique is important for early diagnosis, follow-up and therapy evaluation of gastric cancer in clinic. But there are still many problems in gene therapy of gastric cancer. Conclusion Gene detection and gene therapy will become important supplementary means for diagnosis and treatment of 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 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.