Assessing the impact of tissue devitalization time on genome-wide gene expression analysis in ovarian tumor samples.
Author(s): Dumur CI, Sana S, Ladd AC, Ferreira-Gonzalez A, Wilkinson DS, Powers CN, Garrett CT
Publication: Diagn Mol Pathol, 2008, Vol. 17, Page 200-6
PubMed ID: 18382347 PubMed Review Paper? No
Purpose of Paper
This paper investigated the effects of cold ischemia of up to 120 min at room temperature on RNA quality and gene expression profiles in ovarian tumor tissue specimens.
Conclusion of Paper
RNA purity was not affected by up to 120 min of room temperature storage (cold ischemia time) of the tumor specimen prior to freezing. Gene expression profiles did not differ significantly with cold ischemia time in the serous papillary carcinoma specimens. In teratoma specimens, significant changes in levels of four genes [proopiomelanocortin (POMC), forkhead box G1B (FOXG1B), the X (inactive)-specific transcript (XIST), and cadherin 10 (CDH10)] were found for each of the timepoints examined.
Studies
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Study Purpose
This study investigated the effects of cold ischemia of up to 120 min at room temperature on RNA quality and gene expression profiles in ovarian tumor tissue specimens. Two ovarian tumor tissue specimens (a serous papillary carcinoma and an immature teratoma) were collected at the time of surgical removal and transported to the laboratory within 5 min. Each specimen was divided into 5 pieces and snap-frozen in liquid nitrogen after 0, 15, 30, 60, or 120 minutes at room temperature and then stored at -80°C. RNA was extracted from multiple 10-µm thick frozen sections of tissue using TRIZOL reagent and then subjected to a cleanup process with RNeasy reagents (details not provided). RNA purity was measured by spectrophotometry and a bioanalyzer. Gene expression analysis was performed using HG-U133A microarrays.
Summary of Findings:
RNA purity was not affected by up to 120 min of room temperature storage of tumor specimens, prior to freezing. Gene expression profiles did not differ significantly with cold ischemia time in the serous papillary specimens. There were significant changes in teratoma specimens in four genes (POMC, FOXG1B, XIST, and CDH10) for each of the timepoints examined (P<0.05, all). POMC levels decreased rapidly in the first 15 min of storage and then declined at lower rates for the subsequent timepoints while FOXG1B, XIST, and CDH10 showed significant increases in expression levels within the first 15 min and continued to increase at the same rate throughout the 120 min storage period.
Biospecimens
Preservative Types
- Frozen
Diagnoses:
- Neoplastic - Carcinoma
Platform:
Analyte Technology Platform RNA Automated electrophoresis/Bioanalyzer RNA Tissue microarray RNA Spectrophotometry Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Biospecimen Acquisition Cold ischemia time 0 min
15 min
30 min
60 min
120 min