Gene profiling and bioinformatics analyses reveal time course differential gene expression in surgically resected colorectal tissues

Yamagishi, Aya; Matsumoto, Satoshi; Watanabe, Atsushi; Mizuguchi, Yoshiaki; Hara, Keisuke; Kan, Hayato; Yamada, Takeshi; Koizumi, Michihiro; Shinji, Seiichi; Matsuda, Akihisa; Sasaki, Junpei; Shimada, Takashi; Uchida, Eiji

doi:10.3892/or.2014.3053

Cited by 6 publications

(4 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This indicates the rapid and efficient biomolecule preservation with the PAXgene fixative solution. The similar observation was made previously using another type of fixative RNA Later RNA Stabilization Reagent during collection of resected colorectal tissues: no significant differences in mean RIN scores between the normal and tumour samples were observed 17 .…”

Section: Discussionsupporting

confidence: 83%

“…The warm ischemia is the time between surgical incision and tumour specimen removal 12 , which can trigger the cellular stress response 13 14 . Time between tissue removal and its storage, called cold ischemia, should also be minimized because tumour specimen manipulation and storage can both affect the quality of RNA 15 and can distort the gene expression pattern that is associated with a disease condition within minutes 16 17 . For this reason, it is recommended to keep the cold ischemic time short, about 30 minutes maximally 18 .…”

mentioning

confidence: 99%

See 1 more Smart Citation

The focus on sample quality: Influence of colon tissue collection on reliability of qPCR data

Korenkova

Slyšková

Novosadová

et al. 2016

Sci Rep

View full text Add to dashboard Cite

Successful molecular analyses of human solid tissues require intact biological material with well-preserved nucleic acids, proteins, and other cell structures. Pre-analytical handling, comprising of the collection of material at the operating theatre, is among the first critical steps that influence sample quality. The aim of this study was to compare the experimental outcomes obtained from samples collected and stored by the conventional means of snap freezing and by PAXgene Tissue System (Qiagen). These approaches were evaluated by measuring rRNA and mRNA integrity of the samples (RNA Quality Indicator and Differential Amplification Method) and by gene expression profiling. The collection procedures of the biological material were implemented in two hospitals during colon cancer surgery in order to identify the impact of the collection method on the experimental outcome. Our study shows that the pre-analytical sample handling has a significant effect on the quality of RNA and on the variability of qPCR data. PAXgene collection mode proved to be more easily implemented in the operating room and moreover the quality of RNA obtained from human colon tissues by this method is superior to the one obtained by snap freezing.

show abstract

Section: Discussionsupporting

confidence: 83%

mentioning

confidence: 99%

The focus on sample quality: Influence of colon tissue collection on reliability of qPCR data

Korenkova

Slyšková

Novosadová

et al. 2016

Sci Rep

View full text Add to dashboard Cite

show abstract

“…The results of the current study further underline the impact of tissue ischemia time on gene expression. More recently, it has been reported that in colorectal tissue, 10% of genes were differentially regulated 30 to 120 minutes post-resection, but clustering analysis of tumor samples from cases and time points did not reveal a set of similarly regulated genes across all cases [ 23 ] . Within the current study, hierarchical clustering and ANOVA analysis revealed similar changes in gene expression across both normal and tumor samples although gene expression changes were generally lower in tumor compared with normal tissue.…”

Section: Discussionmentioning

confidence: 99%

“…More likely, differences could be due to sample collection. Yamagishi and colleagues extracted all samples including time point zero from post-surgical tissue, but within this study a colonoscopy sample served as a pre-surgical time point [ 23 ] .…”

Section: Discussionmentioning

confidence: 99%

Identification and Validation of a Potential Marker of Tissue Quality Using Gene Expression Analysis of Human Colorectal Tissue

Lange¹,

Unger²,

Schöppler³

et al. 2015

PLoS ONE

View full text Add to dashboard Cite

Correlative studies have identified numerous biomarkers that are individualizing therapy across many medical specialties, including oncology. Accurate interpretation of these studies requires the collection of tissue samples of sufficient quality. Tissue quality can be measured by changes in levels of gene expression and can be influenced by many factors including pre-analytical conditions, ischemic effects and the surgical collection procedure itself. However, as yet there are no reliable biomarkers of tissue quality at researchers’ disposal. The aim of the current study was to identify genes with expression patterns that fluctuated reproducibly in response to typical post-surgical stress (ischemia) in order to identify a specific marker of tissue quality. All tissue samples were obtained from patients with primary colorectal carcinoma (CRC) (N = 40) either via colonoscopy prior to surgery, or by surgical resection. Surgically resected tissue samples were divided into three groups and subjected to cold ischemia for 10, 20 or 45 minutes. Normal colorectal tissue and CRC tissue was analyzed using microarray and quantitative real-time PCR (qPCR). Comparing changes in gene expression between pre- and post-surgical tissue using microarray analysis identified a list of potential tissue quality biomarkers and this list was validated using qPCR. Results revealed that post-operative ischemia significantly alters gene expression in normal and CRC tissue samples. Both microarray analysis and qPCR revealed regulator of G-protein signaling 1 (RGS1) as a potential marker of CRC tissue quality and eukaryotic translation elongation factor 1 alpha 1 (EEF1A1) as a potential reference gene of post-operative tissue quality. Larger studies with additional time points and endpoints will be needed to confirm these results.

show abstract

Identification and Validation of SLC9A2 as A Potential Tumor Suppressor in Colorectal Cancer: Integrating Bioinformatics Analysis with Experimental Confirmation

Liu,

Yang,

Fang

et al. 2024

CURR MED SCI

View full text Add to dashboard Cite

Gene profiling and bioinformatics analyses reveal time course differential gene expression in surgically resected colorectal tissues

Cited by 6 publications

References 31 publications

The focus on sample quality: Influence of colon tissue collection on reliability of qPCR data

The focus on sample quality: Influence of colon tissue collection on reliability of qPCR data

Identification and Validation of a Potential Marker of Tissue Quality Using Gene Expression Analysis of Human Colorectal Tissue

Identification and Validation of SLC9A2 as A Potential Tumor Suppressor in Colorectal Cancer: Integrating Bioinformatics Analysis with Experimental Confirmation

Contact Info

Product

Resources

About