Discovery and validation of methylated-differentially expressed genes in Helicobacter pylori-induced gastric cancer
- 作者列表："Liu, Duanrui","Ma, Xiaoli","Yang, Fei","Xiao, Dongjie","Jia, Yanfei","Wang, Yunshan
DNA methylation has an important role in Helicobacter pylori ( H. pylori )-induced gastric cancer (GC) processes and development. The aim of this study was to search genome-scale epigenetic modifications for studying pathogenesis of H. pylori- induced GC, and to find factors and powerful signature related to survival and prognosis. In this study, we conducted a comprehensive analysis of DNA methylation and gene expression profiles in the Gene Expression Omnibus (GEO), to identified differentially expressed genes (DEGs) and differentially methylated genes (DMGs). Functional enrichment analysis of the screened genes was performed, and a protein–protein interaction network was constructed. The TCGA DNA methylation databases and 55 H. pylori -infected GC cases of GEO RNA sequencing (GSE62254) were utilized for prognostic value validation of hub genes. Finally, a prognosis-related risk signature was identified by a series of bioinformatics analysis for H. pylori -induced GC patients. Totally, 161 DMGs were identified. Pathway analysis showed that all MDEGs mainly associated with Ras signaling pathway, renal cell carcinoma, mitogen-activated protein kinase signaling pathway. Five hub genes including CACNB2, GNB4, GRIN2A, MEF2C, and PREX1 were screened as independent prognostic factors in H. pylori -induced GC patients. Two-gene (CACNB2 and MEF2C) risk signature was constructed for predicting the overall survival of H. pylori -induced GC patients. Our study indicated possible MDEGs and pathways in H. pylori -induced GC by bioinformatics analysis, which may provide novel insights for unraveling pathogenesis of H. pylori- induced GC. Hub genes might serve as aberrantly methylation-based biomarkers for clinical diagnostic and prognostic evaluation of H. pylori -induced GC.
DNA 甲基化在幽门螺杆菌 (H. pylori) 诱导的胃癌 (GC) 过程和发展中具有重要作用。本研究的目的是搜索用于研究 H. pylori 诱导 GC 的发病机制的基因组规模表观遗传修饰，并找到与生存和预后相关的因素和强大的签名。在这项研究中，我们对基因表达综合 (GEO) 中的 DNA 甲基化和基因表达谱进行了全面分析，以鉴定差异表达基因 (DEGs) 和差异甲基化基因 (DMGs)。对筛选出的基因进行功能富集分析，构建了蛋白质-蛋白质相互作用网络。利用 TCGA DNA 甲基化数据库和 55 例 H. pylori 感染的 GC 病例的 GEO RNA 测序 (GSE62254) 进行 hub 基因的预后价值验证。最后，通过对 H. pylori 诱导的 GC 患者进行一系列生物信息学分析，确定了预后相关的风险特征。共鉴定出 161 个 dmg。通路分析显示，所有 MDEGs 主要与 Ras 信号通路、肾细胞癌、丝裂原活化蛋白激酶信号通路相关。筛选了 CACNB2 、 GNB4 、 GRIN2A 、 MEF2C 和 PREX1 等 5 个 hub 基因作为 H. pylori 诱导的 GC 患者的独立预后因素。构建了双基因 (CACNB2 和 MEF2C) 风险标记用于预测 H. pylori 诱导的 GC 患者的总生存期。我们的研究通过生物信息学分析指出了 H. pylori 诱导的 GC 中可能的 MDEGs 和通路，这可能为解开 H. pylori 诱导的 GC 的发病机制提供新的见解。Hub 基因可能作为基于异常甲基化的生物标志物，用于 H. pylori 诱导的 GC 的临床诊断和预后评估。
METHODS::Diffuse gastric cancer (DGC) is a lethal malignancy lacking effective systemic therapy. Among the most provocative recent results in DGC has been that the alter of the cellular cytoskeleton and intercellular adhesion. CD2-associated protein (CD2AP) is one of the critical proteins regulating cytoskeleton assembly and intercellular adhesion. However, no study has investigated the expression and biological significance of CD2AP in gastric cancer (GC) to date. Therefore, the aim of our study was to explore if the expression of CD2AP is associated with any clinical features of GC and to elucidate the underlying mechanism. Immunohistochemistry of 620 patient tissue samples indicated that the expression of CD2AP is downregulated in DGC. Moreover, a low CD2AP level was indicative of poor patient prognosis. In vitro, forced expression of CD2AP caused a significant decrease in the migration and invasion of GC cells, whereas depletion of CD2AP had the opposite effect. Immunofluorescence analysis indicated that CD2AP promoted cellular adhesion and influenced cell cytoskeleton assembly via interaction with the F-actin capping protein CAPZA1. Overall, the upregulation of CD2AP could attenuate GC metastasis, suggesting CD2AP as a novel biomarker for the prognosis and treatment of patients with GC.
METHODS::Aim: To identify the methylated-differentially expressed genes (MDEGs) that may serve as diagnostic markers and therapeutic targets in Epstein-Barr virus-associated gastric cancer (EBVaGC) and to explore the methylation-based pathways for elucidating biological mechanisms of EBVaGC. Materials & methods: Gene expression and methylation profiles were downloaded from GEO database. MDEGs were identified by GEO2R. Pathway enrichment analyses were conducted based on DAVID database. Hub genes were identified by Cytoscape, which were further verified by The Cancer Genome Atlas database. Results: A total of 367 hypermethylated, lowly expressed genes were enriched in specific patterns of cell differentiation. 31 hypomethylated, highly expressed genes demonstrated enrichment in regulation of immune system process. After validation using The Cancer Genome Atlas database, seven genes were confirmed to be significantly different hub genes in EBVaGC. Conclusion: EBVaGC-specific MDEGs and pathways can be served as potential biomarkers for precise diagnosis and treatment of EBVaGC and provide novel insights into the mechanisms involved.
METHODS:Gastric adenocarcinoma, like other cancers, is a multifactorial genetic disease, andmetastasis of cancer cells is one of the main features of this illness. The expressionlevels of the CFL1 gene have been modulated in this pathway. Using small interferingRNA (siRNA) in the treatment of gastric cancer is considered a hopeful genetherapeutic approach. The present study reported the level of CFL1 genes betweentumor and margin and healthy tissue of gastric cancer. Also, the features of a cationicnanoparticle with a polymer coating containing polyacrylic acid and polyethylenei-mine that were used in the delivery of CFL1 siRNA, were shown. Then thecytotoxicity, cellular uptake, and gene silencing efficiency of this nanoparticle wereevaluated with CFL1siRNA. Method:In this study, the CFL1 gene expression was measured in 40 gastricadenocarcinoma, marginal and 15 healthy biopsy samples by a real‐time polymerasechain reaction. Physicochemical characteristics, apoptosis, and inhibition of migrationof the delivery of CFL1 siRNA by nanoparticle and lipofectamine were investigated ingastric cancer cells. Result:The CFL1 expression was remarkably increased in gastric cancer tissues incomparison with the marginal samples and normal tissues (p< .05) and the biomarkerindex for CFL1 was obtained as 0.94, then this gene can be probably used as abiomarker for gastric cancer. After treatment of the AGS cell line by CFL1 siRNA, theCFL1 expression level of mRNA and migration in AGS cells were remarkablysuppressed after transfection. Furthermore, the amount of apoptosis increased(p< .05). Conclusion:Our results demonstrated that CFL1 downregulation in AGS cells caninterdict cell migration. Finally, our outcomes propose that CFL1 can function as anoncogenic gene in gastric cancer and would be considered as a potential purpose ofgene therapy for gastric cancer treatment