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| Status |
Public on Mar 15, 2016 |
| Title |
Digital expression profiling identifies CDC5L, RECQL4, and CDK4 as potential oncogenes in a cohort of pediatric osteosarcoma tumours |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
Osteosarcoma is the most common malignancy of bone, and occurs most frequently in children and adolescents. Currently, the most reliable technique for prognostication is measuring histopathologic tumor necrosis following preoperative chemotherapy, and favourable prognosis is signified by 90% or greater estimated necrosis of the tumour. Neither genetic testing nor molecular biomarkers have been described for this tumour. We used the novel nanoString mRNA expression analysis system to analyzed total RNA from 35 flash-frozen sporadic paediatric osteosarcoma biopsy and resection specimens to quantify mRNA expression for 17 oncogenes and tumour suppressor genes. Three oncogenes, cell cycle regulator gene CDC5L, the RecQ DNA helicase gene RECQL4, and the cyclin-dependent kinase gene CDK4, were more highly expressed (p<0.05) in tumours which responded poorly to neoadjuvant chemotherapy. A similar trend (p<0.10) was identified for the osteoblast-specific transcription factor gene RUNX2. No statistically significant difference existed in comparing expression of CDC5L, RECQL4, CDK4, and RUNX2 between biopsy and resection samples. Additionally, analysis of expression data in the context of histological subtype yielded preliminary results for deducing molecular subtypes of osteosarcomas. Osteoblastic osteosarcomas possessed higher expression of CDKN1A, PTEN, and RUNX2 relative to their fibroblastic counterparts (p<0.05). This research study shows that CDC5L, RECQL4, and CDK4 tumour expression levels may be useful for identifying patients who may not benefit from the current standardized chemotherapy regimen.
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| Overall design |
Total RNA was isolated from 52 pediatric osteosarcoma samples (prechemotherapy biopsies and resections), 3 osteosarcoma cell lines, and normal human osteoblasts. nanoString mRNA expression analysis was applied to samples split between 3 batches to compare samples based on clinical and pathologic data reports, and to compare samples with normal human osteoblasts. For 43 samples, there were complete data and the RNA was successfully assayed. Analysis was performed using R.
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| Contributor(s) |
Martin JW, Chilton-MacNeill S, Squire JA, Zielenska M |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Mar 19, 2013 |
| Last update date |
Mar 15, 2016 |
| Contact name |
Jeff W Martin |
| Organization name |
Hospital for Sick Children
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| Street address |
555 University Avenue
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| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M5G 1X8 |
| Country |
Canada |
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| Platforms (1) |
| GPL16814 |
Zielenska Lab custom nanoString nCounter gene expression codeset |
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| Samples (144)
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| Relations |
| BioProject |
PRJNA193395 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE45275_RCCCollectorDataAnalysisGuidelines.pdf.gz |
1.4 Mb |
(ftp)(http) |
PDF |
| GSE45275_raw_signals.txt.gz |
8.7 Kb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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