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The molecular mechanism and clinical significance of IGF2BP3 in adenocarcinoma of the esophagogastric junction [meRIP-seq]

ABSTRACT: To reveal the potential m6A modification gene in Adenocarcinoma of the esophagogastric junction, we performed methylated RNA immunoprecipitation and sequencing (meRIP-seq) in OE-19 cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE261201 | GEO | 2024/10/09

REPOSITORIES: GEO

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The molecular mechanism and clinical significance of IGF2BP3 in adenocarcinoma of the esophagogastric junction [RIP-seq]

Project description:To reveal the potential targets of IGF2BP3 in Adenocarcinoma of the esophagogastric junction, we performed IGF2BP3 Immunoprecipitation sequencing (RIP-seq) in OE-19 cells.

2024-10-09 | GSE261200 | GEO

The molecular mechanism and clinical significance of IGF2BP3 in adenocarcinoma of the esophagogastric junction [RNA-seq]

Project description:To explore the major function of IGF2BP3 in Adenocarcinoma of the esophagogastric junction, we conducted RNA sequencing (RNA-seq) in IGF2BP3 KD OE-19 cells.

2024-10-09 | GSE261202 | GEO

The molecular mechanism and clinical significance of IGF2BP3 in adenocarcinoma of the esophagogastric junction [LACE-seq]

Project description:To reveal the potential targets of IGF2BP3 in Adenocarcinoma of the esophagogastric junction, we performed linear amplification of complementary DNA ends and sequencing (LACE-seq) in OE-19 cells.

2024-10-09 | GSE261199 | GEO

m6A full transcriptome map of human adenocarcinoma of esophagogastric junction

Project description:Here we systematically analyze the modification pattern of m6A mRNA in adenocarcinoma at the esophagogastric junction.In adenocarcinoma of esophagogastric junction samples, a total of 4775 new m6A peaks appeared, and 3054 peaks disappeared. The unique m6A-related genes in adenocarcinoma of esophagogastric junction are related to cancer-related pathways. There are hypermethylated or hypomethylated m6A peaks in AEG in differentially expressed mRNA transcripts. This study preliminarily constructed the first m6A full transcriptome map of human adenocarcinoma of esophagogastric junction. This has a guiding role in revealing the mechanism of m6A-mediated gene expression regulation.

2022-02-18 | GSE189874 | GEO

m6A full transcriptome map of human adenocarcinoma of esophagogastric junction

Project description:m6A full transcriptome map of human adenocarcinoma of esophagogastric junction

| PRJNA784934 | ENA

Gastric and esophagogastric junction adenocarcinoma with infrequent hypermethylation show poor prognosis

Project description:Background Gastric cancer (GC) was characterized by unique DNA methylation epigenotypes (MEs). Still, MEs, including adenocarcinoma of the esophagogastric junction (AEG) and background non-neoplastic columnar mucosae (NM), are yet to be clarified. Methods We analyzed genome-wide DNA MEs of AEG, GC, and background NM using Infinium 450k beadarray, followed by quantitative pyrosequencing validation. Large-scale data of the Cancer Genome Atlas (TCGA) were additionally reviewed. Results Unsupervised two-way hierarchical clustering using Infinium data of 21 AEG, 30 GC, and 11 NM showed four DNA MEs: extremely high-ME (E-HME), high-ME (HME), low-ME (LME), and extremely low-ME (E-LME). The promoter methylation levels were validated by pyrosequencing in 146 samples. Although almost normal mucosae were clustered into E-LME, gastric or esophagogastric junction mucosae with chronic inflammatory change due to either Helicobacter pylori infection or reflux esophagitis were clustered together into LME, which suggested that the inflammation status determined DNA MEs regardless of the causes. Three cases of Barrett’s-related adenocarcinoma were all clustered into HME. Among 94 patients whose tumors can be clustered into one of four MEs, 11 patients with E-LME cancers showed significantly shorter overall survival than the other MEs, even in multivariate Cox regression estimate. TCGA data also showed enrichment of AEG in HME and a poorer prognosis of E-LME. Conclusions E-LME cases, newly confirmed in this study, would be a unique aggressive subtype not associated with the elevation of DNA methylation levels caused by inflammation. LME could be acquired via chronic inflammation independent of the causes, and AEG frequently showed HME.

2022-10-20 | GSE207846 | GEO

Prognostic significance of NFIA and NFIB in esophageal squamous carcinoma and esophagogastric junction adenocarcinoma.

Project description:The nuclear factor I (NFI) family members, especially NFIA and NFIB, play essential roles in cancers. The roles of NFIA and NFIB in esophageal squamous cell carcinoma (ESCC) and esophagogastric junction adenocarcinoma (EJA) remain poorly known. This study aimed to determine the expression of NFIA and NFIB in ESCC and EJA and elucidate their prognostic significance. The expression of NFIA and NFIB was examined in 163 ESCC samples and 26 EJA samples by immunohistochemistry. The results showed that high NFIA expression correlated significantly with poor differentiation, lymph node metastasis, and advanced TNM stage in patients with ESCC. High NFIB expression only correlated with poor differentiation in patients with ESCC. Survival analysis showed that NFIA but not NFIB associated with short overall survival (OS) and disease-free survival (DFS) of patients with ESCC. On the other hand, high NFIB expression correlated with lymph node metastasis, advanced TNM stage, and short OS and DFS in patients with EJA. Finally, multivariate analysis demonstrated that high NFIA expression was an independent prognostic factor for ESCC. Taken together, these results demonstrated that NFIA and NFIB could serve as prognostic indicators for ESCC and EJA, respectively.

| S-EPMC5943462 | biostudies-literature

Integrative proteomic characterization of adenocarcinoma of esophagogastric junction.

Project description:The incidence of adenocarcinoma of the esophagogastric junction (AEG) has been rapidly increasing in recent decades, but its molecular alterations and subtypes are still obscure. Here, we conduct proteomics and phosphoproteomics profiling of 103 AEG tumors with paired normal adjacent tissues (NATs), whole exome sequencing of 94 tumor-NAT pairs, and RNA sequencing in 83 tumor-NAT pairs. Our analysis reveals an extensively altered proteome and 252 potential druggable proteins in AEG tumors. We identify three proteomic subtypes with significant clinical and molecular differences. The S-II subtype signature protein, FBXO44, is demonstrated to promote tumor progression and metastasis in vitro and in vivo. Our comparative analyses reveal distinct genomic features in AEG subtypes. We find a specific decrease of fibroblasts in the S-III subtype. Further phosphoproteomic comparisons reveal different kinase-phosphosubstrate regulatory networks among AEG subtypes. Our proteogenomics dataset provides valuable resources for understanding molecular mechanisms and developing precision treatment strategies of AEG.

| S-EPMC9922290 | biostudies-literature

Prognostic Significance of CIP2A in Esophagogastric Junction Adenocarcinoma: A Study of 65 Patients and a Meta-Analysis.

Project description:BackgroundThe expression of the cancerous inhibitor protein phosphatase 2A (CIP2A) appears to be predictive of the prognosis of various solid tumors. However, the association between this protein and the risk of esophagogastric junction adenocarcinoma (EGJA) remains unclear. We investigated CIP2A expression and its clinical significance in EGJA and conducted a meta-analysis to explore the relationship between CIP2A and the prognosis of patients with solid tumors.MethodsImmunohistochemistry (IHC) was performed to detect the expression of CIP2A in EGJA. Kaplan-Meier estimation, Cox analysis, and ROC curves were performed to analyze the survival of patients and the prognostic factors. In the meta-analysis, we searched relevant publications in several widely used databases and used 15 studies (2348 patients).ResultsIHC demonstrated that CIP2A was elevated in EGJA and correlated with poor survival as an independent indicator. It could forecast the survival more precisely when combined with the grade, which is another independent prognosis marker of EGJA. Meta-analysis demonstrated that the associations between the expression of CIP2A and the prognosis were detected for overall survival (HR = 1.98, 95%CI = 1.69-2.32), disease-specific survival (HR = 1.72, 95%CI = 1.50-1.97), and time to tumor progression (pooled HR = 1.95, 95%CI = 1.56-2.43).ConclusionHigh expression of CIP2A was a poor indicator of the prognosis of EGJA, and CIP2A may be a new biomarker for the diagnosis and treatment of EGJA. The meta-analysis suggested that CIP2A expression can be a predictive marker of overall survival, disease-specific survival, and time to tumor progression in patients with solid tumors.

| S-EPMC6724434 | biostudies-literature

Integrated Proteogenomic Characterization of Adenocarcinoma of the esophagogastric junction

Project description:In this study, we performed comprehensive genomic, transcriptomic, proteomic, and phosphorylation analysis of tumor tissues and paired normal adjacent tissues (NATs) of AEG. we describe integrative proteogenomic analyses of the largest cohort to date of AEG samples that focused particularly on novel and clinically actionable insights revealed in the proteome and Phosphorylation modifications. The data may improve current knowledge about AEG and contribute to its diagnosis, prognosis and drug development.

2022-11-14 | PXD030725 | Pride

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