ObjectiveTo explore the relationship between aberrant promoter CpG islands methylation status of E-cadherin gene and hepatocarcinogenesis, and to assess its significance in clinical early diagnosis of hepatocellular carcinoma (HCC). MethodsSurgically resected specimens, among which cancerous and corresponding noncancerous liver tissues from 34 HCC patients, 10 liver cirrhosis from patients without HCC and normal liver tissues from 4 accidental deaths, were collected in West China Hospital. Breast cancer cell line MDA-MB-435 with promoter CpG islands hypermethylation of E-cadherin as positive control was gained from the Cell Bank of Chinese Academy of Sciences in Shanghai. The methylation status of promoter CpG island of E-cadherin gene was detected by nested methylationspecific polymerase chain reaction (nested-MSP). ResultsE-cadherin gene promoter CpG islands hypermethylation was found in 61.76% (21/34) of cancerous tissues, in 29.41% (10/34) of noncancereous tissues from the 34 HCC patients and in 50.00% (5/10) liver cirrhosis from patients without HCC. None of the 4 normal liver samples were detected E-cadherin mehylation positive. Moreover, the methylation of E-cadherin gene was significantly more frequent in 34 cancerous than that in corresponding noncancerous liver tissues (Plt;0.05), which had no significant difference between the 10 cirrhotic samples and cancerous or non-cancerous liver tissues (Pgt;0.05). In 34 cancerous samples, with the combination of both biomarkers of E-cadherin methylation and AFP400 (serum AFP level at a cutoff of 400 μg/L), the diagnostic sensitivity of HCC increased to 82.35%. ConclusionsThe aberrant promoter methylation of E-cadherin gene may play a vital role in the development and progression of HCC. Moreover, it might be an early event in hepatocarcinogensis. It is of high value to make further study to confirm the significance of E-cadherin gene methylation in clinical diagnosis and therapy.
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.
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.
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.
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.
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.
Diabetic retinopathy (DR) is one of the most common microvascular complications of diabetes, characterized by high blindness rates and a severe impact on patients' quality of life. Despite adequate glycemic control, some patients exhibit persistent progression of retinal microvascular damage, known as the "metabolic memory" phenomenon. Studies have revealed that the essence of this phenomenon is the sustained expression of epigenetic reprogramming induced by metabolic stress, in which abnormal mitochondrial DNA (mtDNA) methylation plays a pivotal role. Metabolic abnormalities such as hyperglycemia, hyperhomocysteinemia, and hyperlipidemia can alter mtDNA methylation patterns, triggering cascading pathological processes including oxidative stress, chronic inflammation, and neurovascular network disorders, remodeling mitochondrial energy metabolism, and promoting the evolution of DR from subclinical compensatory stage to irreversible structural damage. Abnormal mtDNA methylation serves as a hallmark of metabolic memory and a core driver of microvascular lesions, providing an important theoretical basis for in-depth analysis of metabolic memory mechanisms and exploration of DR intervention strategies. Current research needs to further elucidate its role in DR. Future efforts require integration of multi-dimensional epigenetic biomarkers, precise intervention approaches, and clinical translational research to advance the early diagnosis and individualized treatment of DR.
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.
