ABSTRACT
【Objective】 To explore the differentially expressed genes in normal prostate and prostate cancer (PCa) tissues based on bioinformatics and screen out potential biomarkers for PCa, so as to provide scientific basis for later clinical medicine. 【Methods】 Three gene chip datasets of GSE55945, GSE46602 and GSE69223 were downloaded from GEO database, and differentially expressed genes (DEGs) were screened by the OmicStudio tools, and protein-protein interaction network (PPI) of DEGs was constructed by STRING. After Cytoscape was imported, CytoHubba plug-in was used to screen the top 30 genes in MCC score as key genes (Hub gene). DAVID was used for GO and KEGG enrichment analysis of Hub gene, and GraphPad Prism software was used to draw ROC curve. GEPIA database was used to verify the key genes, and survival analysis was further carried out. UALCAN was used to verify the correlation between the expression of key genes and Gleason grade of PCa. 【Results】 Three data sets (GSE55945, GSE46602 and GSE69223) obtained 428, 727 and 1285 differentially expressed genes, respectively. The Venn diagram shows that the three datasets contain 105 DEGs. Among 105 PPI networks corresponding to DEGs, the top 30 genes with MCC score were selected as Hub genes. The biological processes involved mainly include the positive regulation of protein kinase B signal, cell differentiation, positive regulation of transcription, negative regulation of transforming growth factor β receptor signaling pathway, positive regulation of cell migration, etc. The pathways involved are adhesion plaque, estrogen signaling pathway, etc. ROC curve results showed that the diagnostic ability of 9 genes in 3 data sets was statistically significant, and 9 Hub genes were CAV1, KDR, CAV2, TGFBR1, SLC7A11, GSTM2, GSTM3, GSTM5 and MYO6. Nine Hub genes were verified by GEPIA website, among which CAV1, KDR, CAV2, TGFBR1, GSTM2, GSTM3 and GSTM5 showed low expression in PCa, while SLC7A11 and MYO6 showed high expression in PCa. Survival analysis suggested that high GSTM5 expression prolonged OS in PCa patients. UALCAN results showed that the expression of GSTM5 gene was significantly correlated with Gleason grade, and the expression of GSTM5 gene decreased with the increase of Gleason score. 【Conclusion】 Hub genes CAV1, KDR, CAV2, TGFBR1, GSTM2, GSTM3 and GSTM5 are low expression in PCa, while SLC7A11 and MYO6 are high expression in PCa. GSTM5 gene is related to the survival rate of PCa. The expression of GSTM5 decreased with the increase of Gleason score, which indicated that GSTM5 may be a potential biomarker for PCa.
ABSTRACT
Objective:To investigate the role of methylation status of glutathione transferase mu5 (GSTM5) promoter region in the occurrence and development of myelodysplastic syndrome (MDS) and provide a new potential molecular marker for the early diagnosis of MDS.Method:Bone marrow blood samples were collected from 40 patients with initial diagnosis of MDS [5 cases of MDS with single dysplasia (MDS-SLD), 7 cases of MDS with multilineage dysplasia (MDS-MLD), 6 cases of MDS with ringed sideroblasts (MDS-RS), 13 patients with refractory with excess blast-1 (RAEB1), 9 patients with refractory with excess blast-2 (RAEB2)], 8 patients with AML secondary to MDS and 6 patients with non-malignant blood diseases(4 patients with iron deficiency anemia and 2 patients with nutritional megaloblastic anemia) in PLA General Hospital from October 2018 to June 2021. Methylation status of the promoter region of GSTM5 gene in three groups were detected by the Agena MassArray nucleic acid mass spectrometry. The Wilcoxon nonparametric test (non-normally distributed data, median (IQR)] was used to compare the methylation levels of GSTM5 gene in different groups. Receiver operating characteristic (ROC) curve was used to evaluate the specificity, sensitivity and accuracy of the test.Results:Cluster analysis showed that the methylation status of GSTM5 in MDS group was higher than that in control group [0.50 (0.27, 0.79) vs.0.29(0.10, 0.45), P<0.05]; The methylation status of GSTM5 in sAML group was significantly higher than that in MDS group [0.67 (0.36, 0.86) vs. 0.50 (0.27, 0.79), P<0.05].The differences in the methylation status of each CpG site were analyzed, and there were statistically significant differences between the MDS group and the control group at CpG_1, CpG_4, 5, CpG_6, 7, 8, CpG_11, CpG_13, 14, CpG_15, CpG_16, CpG_22 and CpG_24 sites ( P<0.05). The results of ROC curve analysis showed that the area under the CpG_6, 7, 8 site curves was the largest, with AUC=0.861(95% CI 0.717-1.000; P<0.05), and the sensitivity and specificity were 85% and 83%, respectively. By analyzing the relationship between GSTM5 methylation and MDS disease development, GSTM5 methylation levels were significantly increased in the higher bone marrow blast group and the high-risk subgroup (RAEB). Conclusion:Aberrant DNA promoter methylation of GSTM5 was a frequent event in MDS and may play an important role in the occurrence and development of MDS. It might be served as a promising biomarker in the diagnosis of MDS.
ABSTRACT
BACKGROUND: Myelodysplastic syndrome (MDS) is a preleukemic condition that transforms into acute myeloid leukemia. However, the genetic events underlying this transformation remain poorly understood. Aberrant DNA methylation may play a causative role in the disease and its prognosis. Thus, we compared the DNA methylation profiles in refractory anemia with excess blast (RAEB) to those in refractory cytopenia with multilineage dysplasia (RCMD). METHODS: Bone marrow samples were collected from 20 patients with primary MDS (9 with RAEB and 11 with RCMD), and peripheral blood samples were collected from 4 healthy controls. These samples were assessed using a commercial whole genome-wide methylation assay. Methylation-specific polymerase chain reaction (PCR) was used to detect the methylation of candidate gene promoters in RAEB and RCMD. RESULTS: Microarray data revealed significant hypermethylation in 69 genes within RAEB but not RCMD. Candidate genes were mapped to 5 different networks, and network 1 had the highest score due to its involvement in gene expression, cancer, and cell cycle. Five genes (GSTM5, BIK, CENPH, RERG, and ANGPTL2) were associated with malignant disease progression. Among them, the methylated promoter pairs of GSTM5 (55.5% and 20%), BIK (20% and 0%), and ANGPTL2 (44.4% and 10%) were observed more frequently in RAEB. CONCLUSION: DNA methylation of GSTM5, BIK, and ANGPTL2 may induce epigenetic silencing and contribute to the increasing blasts and resulting MDS progression; however, the functions of these genes were not determined. Further study focusing on epigenetic silencing using various detection modalities is required.