Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomics analysis report of benign esophageal stricture

ABSTRACT: Esophageal stricture (ES), there is no effective drug and treatment to cure or cure ES. Here, we report the analysis of corresponding biopsy tissues from ES patients and non-ES patients based on high-resolution proteomics, revealing proteins differentially expressed in ES. This study provides a molecular basis for the search for potential treatment of ES.

ORGANISM(S): Homo Sapiens

SUBMITTER: Yabin Zhu

PROVIDER: PXD042273 | iProX | Tue May 16 00:00:00 BST 2023

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Similar Datasets

Genome-wide expression from the esophageal biopsies of subjects with and without eosinophilic esophagitis

Project description:Esophageal biopsy RNA was isolated from distal esophageal biopsy RNA from EoE patients with active disease and from unaffected controls. EoE biopsies showed active disease pathology at the time when they were taken, and all patients reported no glucocorticoid treatment at the time of biopsy. RNA sequencing acquiring 50 million mappable 125 base-pair reads from paired-end libraries was performed at the Genetic Variation and Gene Discovery Core Facility at Cincinnati Children's Hospital Medical Center. Data were aligned to the hg19 build of the human genome using the Ensembl annotations as a guide for TopHat.

2019-06-16 | GSE113341 | GEO

Potential proteins identification for stent restenosis induced by esophageal benign hyperplasia in esophageal cancer

Project description:This study was conducted to explore the potential proteins associated with esophagus benign hyperplasia induced by esophageal stents.

2023-03-10 | PXD014242 | Pride

Increased plasma matrix metalloproteinase 1 is associated with the presence of esophageal squamous cell carcinoma

Project description:Esophageal squamous cell carcinoma (ESCC) patients are usually diagnosed at late stages, prohibiting the chance of surgical cure. The obstacle partly comes from the lack of molecular markers for early detection. Moreover, there is no consensus about endoscopic surveillance for ESCC. This study aimed to identify noninvasive markers for ESCC detection. By microarray-based screening of 17 pairs of human ESCC specimens, we identified that secreted protein matrix metalloproteinase-1 (MMP1) may be associated with the presence of ESCC. The tumor and adjacent normal tissues were obtained from 17 male ESCC patients who underwent total esophagectomy without previous cancer treatment at Kaohsiung Medical University Hospital (KMUH)

2015-07-01 | E-GEOD-70409 | biostudies-arrayexpress

Oncoscan SNP-array analysis of DNA from esophageal samples of patients with Barrett's esophagus before and after progression to esophageal dysplasia and adenocarcinoma

Project description:The goal of this experiment is to characterize the copy number changes in esophageal mucosa of patients with Barrett's esophagus (BE) who progress to esophageal dysplasia and adenocarcinoma (BE progressors), as compared to patients with BE who do not progress for at least two years after esophageal mucosal sampling (non-progressors with never dysplastic Barrett's esophagus - NvDBE - samples). We sampled esophageal mucosa from the following groups: 1) non-dysplastic intestinal metaplasia from 16 patients at least 1 year before progression to esophageal dysplasia or adenocarcinoma (PP-BE); 2) non-dysplastic intestinal metaplasia from 21 patients who did not progress to dysplasia or adenocarcinoma for at least 2 years of surveillance after the tested sample (NvDBE) 3) non-dysplastic intestinal metaplasia from 21 patients who had temporally concurrent but spatially separate intestinal metaplasia samples from the same procedure (C-BE). 4) 10 samples of esophageal dysplasia or adenocarcinoma from patients in group 1 and 3. Samples were obtained by endoscopic biopsy, endomucosal resection or surgical resection, processed for clinical purposes by routine histopathologic methods, including formalin fixation and paraffin embedding (FFPE). DNA was extracted from 5 micro tissue sections of FFPE blocks and DNA extracted using QIAamp DNA FFPE Tissue Kit (Qiagen, Germantown, MD). Samples were processed for identification of somatic copy number alterations using the OncoScan FFPE Assay or the OncoScan CNV Assay (Affymetrix, Santa Clara, CA) according to the manufacturer's protocols. After hybridization, the arrays were washed, stained using GeneChip Fluidics Station 450 (Affymetrix) and scanned using GeneChip Scanner 3000 7G (Affymetrix). The CEL files generated are deposited here.

2019-10-27 | E-MTAB-7396 | biostudies-arrayexpress

Human esophageal dysplasia (16 cases) vs. esophageal squamous cell carcinoma (59 cases)

Project description:Our aim is to identify frequent genomic aberrations both in ESCC and esophageal dysplasia, and to discover important copy number-driving genes and microRNAs in ESCC. We carried out array-based comparative genomic hybridization (array CGH) on 59 ESCC resection samples and 16 dysplasia biopsy samples. Expression of genes at 11q13.3 was analyzed by real-time PCR and immunohistochemistry (IHC). Integrated analysis was performed to identify genes or microRNAs with copy number-expression correlations. Two group experiment, esophageal dysplasia vs. esophageal squamous cell carcinoma. Biological replicates: 16 dysplasias vs. 59 carcinomas

2013-04-29 | E-GEOD-46452 | biostudies-arrayexpress

A novel gene expression signatures associated with the response to concomitant chemo-radiation therapy in patients with esophageal squamous cell carcinoma

Project description:In this study, esophageal squamous cell carcinoma (ESCC) patients’ endoscopic biopsy tumor tissues obtained before their concomitant chemo-radiation therapy (CCRT) were used to analyze the transcriptomes by using the RNA-sequencing approach. According to retrospective study of patients’ responses to CCRT, the treatment-naive specimen can be divided into two groups (16 good CCRT response and 12 poor CCRT response). This systematic profiling uncovered a gene set that is differentially expressed between the two patient groups.

2022-11-02 | GSE199630 | GEO

Transcriptomic profiling of esophageal epithelium reveals enrichment of IFN-γ response gene signature during active EoE.

Project description:Eosinophilic esophagitis (EoE) is a chronic, allergic inflammatory disease of the esophageal mucosa. Although type 2 cytokines are predominant, targeting type 2 inflammation alone is not always effective for all patients. In EoE patients, the transcriptional profiling of esophageal biopsy reveals upregulation of type I and II interferon (IFN) response, dysregulated immune signaling, and downregulation of esophageal-specific genes. However, further investigation is needed to examine the gene expression changes in esophageal epithelium because it plays an important role in EoE. To investigate the upregulation of Interferon Stimulated Genes (ISGs) in EoE esophageal epithelium, we isolated epithelial cells from active EoE patients and non-EoE controls. We performed bulk RNA sequencing to analyze the epithelial-specific transcriptome in EoE. Unsupervised hierarchical clustering of the most variable genes differentiated the active EoE biopsies from non-EoE controls. Gene set enrichment analysis identified IFN-γ response as the most significant upregulated pathway.

2024-02-26 | GSE234973 | GEO

Effect of IFN-α and IFN-γ on gene expression of 3D organoids derived from telomerase-immortalized normal human esophageal keratinocyte cell line, EPC2-hTERT.

Project description:Eosinophilic esophagitis (EoE) is a chronic, allergic inflammatory disease of the esophageal mucosa. While type 2 cytokines are predominant, targeting type 2 inflammation alone is not always effective for all patients. In EoE patients, the transcriptional profiling of esophageal biopsy reveal upregulation of type I and II interferon (IFN) response, dysregulated immune signaling and downregulation of esophageal-specific genes in EoE patients. However, the role of interferon signaling during EoE is not fully understood. This study aims to investigate the impact of IFN signaling on esophageal epithelium and elucidate its role in EoE. IFN-γ stimulation of esophageal epithelial cells triggered disruption of tissue differentiation, epithelial barrier integrity and cytotoxicity, which are relevant features of EoE immunopathology. Beyond EoE, our findings offer insights into esophageal disorders which may involve increased IFN-γ signaling, including infections, gastrophageal reflux disease, and Barrett's esophagus.

2024-02-26 | GSE234424 | GEO

Definition of a multi-omics signature for Esophageal Adenocarcinoma prognosis prediction [totalRNA-seq]

Project description:Esophageal cancer, a highly lethal tumor, contributes to 5% of all cancer deaths, with its primary subtypes being esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC). While most studies focus on ESCC, this study investigates EAC using single-cell RNA sequencing (scRNA-seq) to analyze CD45+ immune cells from tumors and matched non-tumor tissues in therapy-naïve patients. By examining the transcriptional profiles of these immune cells and the entire transcriptome in a cohort of 23 patients, the study identifies distinct transcriptional signatures. These signatures were used to stratify a large cohort of TCGA EAC patients, revealing strong associations with prognosis and clinical outcomes. The findings suggest that these transcriptional profiles can improve prognosis accuracy post-surgery and potentially guide effective therapies, including immunotherapy, for EAC patients.

2024-08-02 | GSE273848 | GEO

Definition of a multi-omics signature for Esophageal Adenocarcinoma prognosis prediction [scRNA-seq]

2024-08-02 | GSE273847 | GEO