Stability and Heterogeneity of Expression Profiles in Lung Cancer Specimens Harvested Following Surgical Resection
Author(s): Blackhall Fiona H, Pintilie Melania, Wigle Dennis A, Jurisica Igor, Liu Ni, Radulovich Nikolina, Johnston Michael R, Keshavjee Shaf, Tsao Ming-Sound
Publication: Neoplasia, 2004, Vol. 6, Page 761
PubMed ID: 15720802 PubMed Review Paper? No
Purpose of Paper
Conclusion of Paper
Studies
-
Study Purpose
The purpose of this study was to determine if gene expression is altered after storage at room temperature (0, 5, 10, 15, 20, 30 , 40 50, 60, 120 min of cold ischemia) following surgical resection prior to snap freezing. Tumor specimens from two patients were used for analysis.
Summary of Findings:
Of the 623 genes investigated via microarray there was no clear linear relationship between altered gene expression and delayed processing time. Real-time qRT-PCR analysis of six stress and hypoxia-induced genes (mitogen-activated protein/MAPK10, JNK3; JUN-B proto oncogene, JUN-B; c-Jun proto oncogene, AP-1; carbonic anhydrase IX, CAIX; protease, serine 25, PRSS25; human homologue of Rad6B, HHR6B) confirmed results of the microarray, suggesting that a delay at room temperature of up to 2 h prior to freezing does not alter gene expression.
Biospecimens
Preservative Types
- Frozen
Diagnoses:
- Neoplastic - Carcinoma
Platform:
Analyte Technology Platform RNA DNA microarray RNA Real-time qRT-PCR Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Biospecimen Acquisition Cold ischemia time 5 min
10 min
15 min
20 min
30 min
40 min
50 min
60 min
120 min
Real-time qRT-PCR Specific Targeted nucleic acid JNK3
JUN-B
AP-1
CAIX
PRSS25
HHR6B
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Study Purpose
The purpose of this study was to assess the effect of tumor heterogenity on global and stress and hypoxia-induced gene expression. A total of 6 samples were collected from each of 4 tumors.
Summary of Findings:
Gene expression (JNK3, JUNB, AP-1, CAIX, HHR6B, PRSS25) varied widely among the 6 intratumoral samples collected from each of the 4 tumors examined. Variance for all genes except HHR6B was greater among intratumoral samples than those samples subjected to 5-120 min of cold ischemia. Interestingly, gene expression was not correlated to the position of sampling (tumor periphery versus core).
Biospecimens
Preservative Types
- Frozen
Diagnoses:
- Neoplastic - Carcinoma
Platform:
Analyte Technology Platform RNA RT-PCR Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Biospecimen Acquisition Cold ischemia time 50 min
60 min
120 min
5 min
10 min
15 min
20 min
30 min
40 min
Biospecimen Aliquots and Components Biospecimen heterogeneity Biospecimen core
Biospecimen periphery
RT-PCR Specific Targeted nucleic acid JNK3
JUNB
AP-1
CAIX
HHR6B
PRSS25
-
Study Purpose
The purpose of this study was to assess the histopathologic appearance of samples collected from 6 different intratumoral locations ranging from the core of the specimen to the periphery. Tumors from 4 patients were examined, and specimens were snap frozen within 30 minutes of resection.
Summary of Findings:
Individual tumors displayed consistent histopathology regardless of intratumoral location (tumor periphery versus core), with the percentage of cancer cells ranging from 60-80% per sample.
Biospecimens
Preservative Types
- Frozen
Diagnoses:
- Neoplastic - Carcinoma
Platform:
Analyte Technology Platform Morphology H-and-E microscopy Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Biospecimen Acquisition Cold ischemia time 40 min
50 min
60 min
120 min
5 min
10 min
15 min
20 min
30 min
Biospecimen Aliquots and Components Biospecimen heterogeneity Biospecimen core
Biospecimen periphery