Potential prognostic impact of EBV RNA-seq reads in gastric cancer: A reanalysis of The Cancer Genome Atlas cohort.
EBV RNA-seq reads 在胃癌中的潜在预后影响: 癌症基因组图谱队列的再分析。
- 作者列表："Sadato D","Ogawa M","Hirama C","Hishima T","Horiguchi SI","Harada Y","Shimoyama T","Itokawa M","Ohashi K","Oboki K
:Epstein-Barr virus (EBV)-associated gastric cancer (EBVaGC), whose prognosis remains controversial, is diagnosed by in situ hybridization of EBV-derived EBER1/2 small RNAs. In the Cancer Genome Atlas (TCGA)-Stomach Adenocarcinoma (STAD) project, the EBV molecular subtype was determined through a combination of multiple next-generation sequencing methods, but not by the gold standard in situ hybridization method. This leaves unanswered questions regarding the discordance of EBV positivity detected by different approaches and the threshold of sequencing reads. Therefore, we re-analyzed the TCGA-STAD RNA-seq dataset including 375 tumor and 32 normal samples, using our analysis pipeline. We defined a reliable threshold for EBV-derived next-generation sequencing reads by mapping them to the EBV genome with three different random arbitrary alignments. We analyzed the prognostic impact of EBV status on the histopathological subtypes of gastric cancer. EBV-positive cases identified by re-analysis comprised nearly half of the cases (49.6%) independent from infiltrating lymphocyte signatures, and showed significantly longer overall survival for adenocarcinomas of the "not otherwise specified" (NOS) type [P = 0.016 (log-rank test); HR 0.476; 95% CI 0.260-0.870, P = 0.016 (Cox univariate analysis)], but shorter overall survival for the tubular adenocarcinoma type [P = 0.005 (log-rank test); HR 3.329; 95% CI 1.406-7.885, P = 0.006 (Cox univariate analysis)]. These results demonstrate that the EBV-positivity rates were higher when determined by RNA-seq than when determined by EBER1/2 in situ hybridization. The RNA-seq-based EBV-positivity demonstrated distinct results for gastric cancer prognosis depending on the histopathological subtype, suggesting its potential to be used in clinical prognoses.
: Eb病毒 (EBV) 相关胃癌 (EBVaGC)，其预后仍存在争议，通过 EBV 衍生的 EBER1/2 小 rna 的原位杂交诊断。在癌症基因组图谱 (TCGA)-胃腺癌 (STAD) 项目中，通过多种新一代测序方法的组合确定了 EBV 分子亚型, 但不能用金标准原位杂交法。这就留下了关于不同方法检测到的 EBV 阳性的不一致性和测序读数阈值的未回答的问题。因此，我们使用我们的分析管道重新分析了包括 375 例肿瘤和 32 例正常样本的 TCGA-STAD RNA-seq 数据集。我们通过将它们映射到具有三种不同的随机任意比对的 EBV 基因组，为 EBV 衍生的下一代测序 reads 定义了一个可靠的阈值。我们分析了 EBV 状态对胃癌组织病理学亚型的预后影响。重新分析确定的 EBV 阳性病例占病例的近一半 (49.6%)，独立于浸润淋巴细胞标记, “未另行指定” (NOS) 型腺癌的总生存期显著延长 [P = 0.016 (log-rank 检验); HR 0.476; 95% CI 0.260-0.870, P = 0.016(Cox 单因素分析)]，但管状腺癌类型的总生存期较短 [P = 0.005 (log-rank 检验); HR 3.329; 95% CI 1.406-7.885, P = 0.006 (Cox 单因素分析)]。这些结果表明，RNA-seq 测定的 EBV 阳性率高于 EBER1/2 原位杂交测定的阳性率。基于 RNA-seq 的 EBV 阳性根据组织病理学亚型证明了胃癌预后的不同结果，提示其用于临床预后的潜力。
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