Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Artificially induced epithelial-mesenchymal transition in surgical subjects: its implications in clinical and basic cancer research

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE32700: Overall aiEMT in non-cancerous samples of esophageal cancer patients GSE32701: Individual aiEMT in surgical samples of esophageal cancer patients Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Kazuhiko Aoyagi

PROVIDER: E-GEOD-22954 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Artificially induced epithelial-mesenchymal transition in surgical subjects: its implications in clinical and basic cancer research.

Aoyagi Kazuhiko K Minashi Keiko K Igaki Hiroyasu H Tachimori Yuji Y Nishimura Takao T Hokamura Norikazu N Ashida Akio A Daiko Hiroyuki H Ochiai Atsushi A Muto Manabu M Ohtsu Atsushi A Yoshida Teruhiko T Sasaki Hiroki H

PloS one 20110421 4

<h4>Background</h4>Surgical samples have long been used as important subjects for cancer research. In accordance with an increase of neoadjuvant therapy, biopsy samples have recently become imperative for cancer transcriptome. On the other hand, both biopsy and surgical samples are available for expression profiling for predicting clinical outcome by adjuvant therapy; however, it is still unclear whether surgical sample expression profiles are useful for prediction via biopsy samples, because li ...[more]

PMID: 21533028

Similar Datasets

Overall aiEMT in non-cancerous samples of esophageal cancer patients

Project description:Surgical samples have long been used as important subjects for cancer research. In accordance with an increase of neoadjuvant therapy, biopsy samples have recently become imperative for cancer transcriptome. On the other hand, both biopsy and surgical samples are available for expression profiling for predicting clinical outcome by adjuvant therapy; however, it is still unclear whether surgical sample expression profiles are useful for the prediction by the use of biopsy samples because little has been done about comparative gene expression profiling between the two kinds of samples. When gene expression profiles were compared between biopsy and surgical samples, artificially induced epithelial-mesenchymal transition (aiEMT) was found in the surgical samples. This study will evoke the fundamental misinterpretation including underestimation of the prognostic evaluation power of markers by overestimation of EMT in past cancer research, and will furnish some advice for the near future as follows: 1) Understanding how long the tissues were under an ischemic condition; 2) Prevalence of biopsy samples for in vivo expression profiling with low biases on basic and clinical research; and 3) Checking cancer cell contents and normal- or necrotic-tissue contamination in biopsy samples for prevalence. We used microarrays to compare gene expression profiles between 5 biopsy (BPY) and 5 surgical (OPE) samples derived from the non-cancerous portion of the esophagus of different esophageal cancer patients.

2011-10-06 | E-GEOD-32700 | biostudies-arrayexpress

Individual aiEMT in surgical samples of esophageal cancer patients

Project description:Surgical samples have long been used as important subjects for cancer research. In accordance with an increase of neoadjuvant therapy, biopsy samples have recently become imperative for cancer transcriptome. On the other hand, both biopsy and surgical samples are available for expression profiling for predicting clinical outcome by adjuvant therapy; however, it is still unclear whether surgical sample expression profiles are useful for the prediction by the use of biopsy samples because little has been done about comparative gene expression profiling between the two kinds of samples. When gene expression profiles were compared between biopsy and surgical samples, artificially induced epithelial-mesenchymal transition (aiEMT) was found in the surgical samples. This study will evoke the fundamental misinterpretation including underestimation of the prognostic evaluation power of markers by overestimation of EMT in past cancer research, and will furnish some advice for the near future as follows: 1) Understanding how long the tissues were under an ischemic condition; 2) Prevalence of biopsy samples for in vivo expression profiling with low biases on basic and clinical research; and 3) Checking cancer cell contents and normal- or necrotic-tissue contamination in biopsy samples for prevalence. We used microarrays to compare gene expression profiles between 20 biopsy (BPY) and 20 surgical (OPE) samples derived from the cancerous portion of the esophagus of 20 esophageal cancer patients. One biopsy sample and one surgical sample was obtained from each patient; these sample pairs have the same number.

2011-10-06 | E-GEOD-32701 | biostudies-arrayexpress

Overall aiEMT in surgical samples of esophageal cancer patients

Project description:Surgical samples have long been used as important subjects for cancer research. In accordance with an increase of neoadjuvant therapy, biopsy samples have recently become imperative for cancer transcriptome. On the other hand, both biopsy and surgical samples are available for expression profiling for predicting clinical outcome by adjuvant therapy; however, it is still unclear whether surgical sample expression profiles are useful for the prediction by the use of biopsy samples because little has been done about comparative gene expression profiling between the two kinds of samples. When gene expression profiles were compared between biopsy and surgical samples, artificially induced epithelial-mesenchymal transition (aiEMT) was found in the surgical samples. This study will evoke the fundamental misinterpretation including underestimation of the prognostic evaluation power of markers by overestimation of EMT in past cancer research, and will furnish some advice for the near future as follows: 1) Understanding how long the tissues were under an ischemic condition; 2) Prevalence of biopsy samples for in vivo expression profiling with low biases on basic and clinical research; and 3) Checking cancer cell contents and normal- or necrotic-tissue contamination in biopsy samples for prevalence. We used microarrays to compare gene expression profiles between 31 biopsy (A, D) and 65 surgical (O) samples derived from the cancerous portion of the esophagus of different esophageal cancer patients.

2011-10-19 | E-GEOD-33103 | biostudies-arrayexpress

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

Expression data from intestinal-type and diffuse-type gastric cancers

Project description:To identify the specific genes for intestinal-type and diffuse-type gastric cancers. We selected 18 intestinal-type gastric cancers and 12 diffuse-type gastric cancers showing typical characteristics on the form of cell growth (clustered or scattered) and the degree of differentiation (well/moderate or poor), and performed microarray analysis for obtaining genome-wide mRNA expression profiles.

2014-12-25 | E-GEOD-47007 | 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

Gene expression profiling in patients with Idiopathic Achalasia

Project description:Comparison of gene expression profiles in 12 resected specimens from achalasia, a rare motility disorder characterized manometrically by the absence of peristalsis and an incompletely relaxing lower esophageal sphincter (LES), patients with those from 5 controls to identify critical genes and highly perturbed pathways with potential involvement in achalasia

2016-02-29 | E-MTAB-3962 | biostudies-arrayexpress

Processed polyA+ RNA sequencing data of tissue samples from patients with esophageal adenocarcinoma or precursor lesions

Project description:In the past decades, the incidence of esophageal adenocarcinoma has increased dramatically in Western populations. Better understanding of disease etiology along with the identification of novel prognostic and predictive biomarkers are urgently needed to improve the dismal survival probabilities. Here, we performed comprehensive RNA (both coding and non-coding) profiling in various samples from 17 patients diagnosed with esophageal adenocarcinoma, high-grade dysplastic or non-dysplastic Barrett’s esophagus. Per patient, a blood plasma sample, and a healthy esophageal and disease tissue sample were included. In total, this comprehensive dataset consists of 102 RNA-seq libraries from 51 samples. The raw data for this study have been deposited to the controlled access archive EGA under submission EGAS00001004939.

2022-01-01 | E-MTAB-10005 | biostudies-arrayexpress

Expression data from esophageal squamous cell carcinomas and normal esophageal epithelia

Project description:Preoperative chemoradiotherapy (CRT) followed by surgery has been proved to improve esophageal squamous cell carcinoma (ESCC) patientsM-bM-^@M-^Y survival in comparison with surgery alone. However, the outcomes of CRT are heterogeneous, and no clinical or pathological method could predict CRT response. We aim to identify mRNA markers for ESCC CRT-response prediction through gene expression analyses. Gene expression analyses were performed on pretreatment cancer biopsies from 28 ESCCs who received neoadjuvant CRT and surgery and 10 normal esophageal epithelia using Affymetrix U133 Plus 2.0 arrays.

2014-08-01 | E-GEOD-45670 | biostudies-arrayexpress

Whole transcriptome profiling of Esophageal adenocarcinoma and Barrett's

Project description:RNA-seq was performed on esophageal adenocarcinoma (EAC), Barrett's without dysplasia, Barrett's with low-grade dysplasia (LGD) and normal squamous esophagus tissue to find early alterations in the transcriptome level turning Barrett's dysplastic.

2017-07-23 | E-MTAB-4054 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data