Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Individual aiEMT in surgical samples of esophageal cancer patients

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE32701 | GEO | 2011/10/07

SECONDARY ACCESSION(S): PRJNA146993

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

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.

2011-10-07 | GSE32700 | GEO

Overall aiEMT in surgical samples of esophageal cancer patients

2011-10-20 | GSE33103 | GEO

Overall aiEMT in non-cancerous samples of esophageal cancer patients

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

Overall aiEMT in surgical samples of esophageal cancer patients

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

Individual aiEMT in surgical samples of esophageal cancer patients

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

Breast Cancer Gene Expression Data from Hamburg Series

Project description:Gene expression profiling of surgical biopsies from 74 breast cancer patients of different subtypes from Hamburg dataset. Fresh frozen pre-treatment surgical biopsy samples from breast cancer patients were analyzed on Affymetrix HGU133A.

2014-04-17 | E-GEOD-46184 | biostudies-arrayexpress

Concordance of DNA methylation profiles between breast core biopsy and surgical excision specimens containing ductal carcinoma in situ (DCIS)

Project description:Whether DNA methylation in ductal carcinoma in situ (DCIS), measured in core biopsy and surgical specimens are similar, remains unclear. Here, we compared genome-scale DNA methylation measured in matched core biopsy and surgical specimens from DCIS, including specific DNA methylation biomarkers of subsequent invasive cancer. This study aims to compare genome-scale DNA methylation between core biopsies (in this GEO accession) and surgical specimens (previously published in GSE66313; see Overall Design below). Within-subject variability in DNA methylation was significantly lower than between-subject variability (all P < 2.20E-16). In 641 CpGs whose methylation was related with increased hazard of invasive breast cancer, lower within-subject than between-subject variability was observed in 92.3% of the study participants (P < 0.05). Between patient-matched core biopsy and surgical specimens, < 0.6% of CpGs measured had changes in median DNA methylation > 15%, and a pathway analysis of these CpGs indicated enrichment for genes related with wound healing. Our results indicate that DNA methylation measured in core biopsies are representative of the matched surgical specimens and suggest that DCIS biomarkers measured in core biopsies can inform clinical decision-making.

2018-02-15 | GSE100503 | GEO

MesoHET (Multi-site tumor sampling highlights molecular intra-tumor heterogeneity in malignant pleural mesothelioma)

Project description:To analyze intra-tumor heterogeneity, DNA methylation was analysed in paired tumor samples of 16 patients from whom biopsies were taken at distinct anatomical sites. Samples were collected from 2014 to 2017 in two French hospitals. All samples obtained from surgical samples or tumor biopsy were immediately frozen in liquid nitrogen and stored at -80°C prior extraction.

2021-06-08 | GSE175769 | GEO

Subcutaneous adipose tissue from lean and obese subjects

Project description:Obtaining adipose tissue samples are paramount to the understanding of human obesity. We have examined the impact of needle-aspirated and surgical biopsy techniques on the study of subcutaneous adipose tissue (scAT) gene expression in both obese and lean subjects. Biopsy sampling methods have a significant impact on data interpretation and revealed that gene expression profiles derived from surgical tissue biopsies better capture the significant changes in molecular pathways associated with obesity. We hypothesize that this is because needle biopsies do not aspirate the fibrotic fraction of scAT; which subsequently results in an under-representation of the inflammatory and metabolic changes that coincide with obesity. This analysis revealed that the biopsy technique influences the gene expression underlying the biological themes commonly discussed in obesity (e.g. inflammation, extracellular matrix, metabolism, etc), and is therefore a caveat to consider when designing microarray experiments. These results have crucial implications for the clinical and physiopathological understanding of human obesity and therapeutic approaches. Keywords: subject and tissue biopsy technique comparison Tissue samples from lean and obese subjects were analyzed: total of 36 hybridizations. The goal was to compare the effect of biopsy sampling methods on global subcutaneous adipose tissue gene expression analyses. The following subject groups were used for the analysis: 9 lean subjects: needle biopsy 9 lean subjects: surgical biopsy 9 obese subjects: needle biopsy 9 obese subjects: surgical biopsy

2008-12-22 | E-GEOD-12050 | biostudies-arrayexpress