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Series GSE2837 Query DataSets for GSE2837
Status Public on Nov 02, 2006
Title Survival Prediction of HNSCC using FFPE samples
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Recently it was shown that gene expression signatures generated from DNA microarray analyses have promise as biomarkers of clinical outcome and that the molecular characteristics of tumors could be elucidated. Through this study, we have determined a high-risk signature for recurrence as a prognostic biomarker using formalin-fixed HNSCC tumors and tested the results to an independent data set obtained from fresh frozen tumors as a comparison. Also, we have shown the genes that are involved in epithelial to mesenchymal transition and nuclear factor-ĸB signaling deregulation are the most prominent molecular characteristics of the high-risk tumors. Forty samples including 34 formalin-fixed tissues and 6 matched frozen tissues from 29 HNSCC patients were analyzed for gene expression. The formalin-fixed tumors were classified based on their gene expression by intrinsic analysis and the intrinsic gene list was tested on the classification of previously published 60 frozen HNSCC tumors which highly correlated. Based on the molecular classification, a 75-gene list that is predictive of high-risk for recurrence was determined by training on the formalin-fixed tumor set and tested on the independent frozen tumor set. The difference in recurrence-free survival (RFS) between the high-risk vs. low-risk groups in the training and test sets were statistically significant (Log-rank test, p=0.002 and p=0.03, respectively). Also, the gene expression data was interrogated using Gene Set Enrichment Analysis to determine functional significance. The most significant sets of genes that are enriched in the high-risk tumors were genes involving epithelial to mesenchymal transition (EMT), NF-ĸB activation and cell adhesion. In conclusion, global gene expression analysis is feasible using formalin-fixed tissue, and the data from different sample preparations and array platforms can be reliably combined for analyses. The 75-gene list can be utilized as a prognostic biomarker of recurrence and the molecular characteristics of EMT and NF-ĸB activation can be targeted as the novel therapy in the identified high-risk patients.
Keywords: FFPE, survival analysis
 
Overall design 34 HNSCC samples from FFPE tissue and 6 HNSCC samples from fresh frozen tissue. Each independtly hybridized using Affymetrix X3P chips.
 
Contributor(s) Chung CH, Parker JS, Ely K, Carter J, Murphy BA, Yi Y, Zanation8 A, Ang KK, El-Naggar AK, Cmelak AJ, Slebos RJ, Levy S, Yarbrough WG
Citation(s) 16912200
Submission date Jun 24, 2005
Last update date Mar 16, 2012
Contact name Christine H. Chung
E-mail(s) christine.chung@vanderbilt.edu
Phone 615-322-4967
Fax 615343-7602
Organization name Vanderbilt University
Department Internal Medicine
Lab Chung
Street address 777 PRB
City Nashville
State/province TN
ZIP/Postal code 37232-6307
Country USA
 
Platforms (1)
GPL1352 [U133_X3P] Affymetrix Human X3P Array
Samples (40)
GSM62201 2004-06-08-300148-Chung-HumanX3P-Rep1
GSM62202 2004-06-08-S0324497-Chung-HumanX3P-Rep1
GSM62203 2004-11-24-CHC74-Chung-HumanX3P-Rep1
Relations
BioProject PRJNA92471

Clinical Data header descriptions
subject
sample ID
array name
age
sex
Treatment
cTNM stage
tumor site
recurrence
RFS (mo)
cause of death

Data table
subject sample ID array name age sex Treatment cTNM stage tumor site recurrence RFS (mo) cause of death
1 MD8E3 2005-06-02-81CC3-Chung-HuX3P-Rep1.CEL 74 M T3N2bM0 OC DOD/DOC
1 MD8E3-frozen 2005-06-02-81CC2-Chung-HuX3P-Rep1.CEL 76 M T3N2bM0 OC DOD/DOC
2 VU36 2004-12-16-CHC85-Chung-HumanX3P-Rep1.CEL 41 F s->xrt/chemo T1N2cM0 L NED 37.8 DOC
3 VU53 2004-11-24-CHC77-Chung-HumanX3P-Rep1.CEL 55 M s->xrt T3N0M0 L NED 76.6 DOC
4 MD147E5 2005-07-19-81CC25-Chung-HuX3P-Rep1.CEL 81 M s->xrt T4N2aM0 L REC 13 DOD/DOC
4 MD147E5-repeat 2005-07-19-81CC26-Chung-HuX3P-Rep1.CEL 82 M s->xrt T4N2aM0 L REC 13 DOD/DOC
4 MD147E5-frozen 2005-07-19-81CC27-Chung-HuX3P-Rep1.CEL 83 M s->xrt T4N2aM0 L REC 13 DOD/DOC
5 VU119 2004-11-24-CHC78-Chung-HumanX3P-Rep1.CEL 44 M s->xrt T1N2bM0 OP NED 105.3 Alive
6 VU132 2004-11-24-CHC76-Chung-HumanX3P-Rep1.CEL 58 M s->xrt/chemo T4N2bM0 OC REC 7.9 DOD
7 VU150 2004-11-24-CHC81-Chung-HumanX3P-Rep1.CEL 60 M s->xrt T2N2bM0 OP NED 80.7 DOC
8 VU291 2004-11-24-CHC74-Chung-HumanX3P-Rep1.CEL 78 M s only T2N0M0 OP REC 5.8 DOC
9 VU232 2004-12-16-CHC83-Chung-HumanX3P-Rep1.CEL 80 M s->xrt/chemo T4N1M0 L REC 27.1 DOD
10 VA248 2005-01-12-CHC91-Chung-HumanX3P-Rep1.CEL 52 M s->xrt T2N1M0 OP REC 4.2 DOD
11 VU260 2004-12-16-CHC84-Chung-HumanX3P-Rep1.CEL 55 M s->xrt/chemo T2N3M0 OP REC 16.5 DOC
12 VU265 2004-11-24-CHC82-Chung-HumanX3P-Rep1.CEL 58 M s->xrt T2N2bM0 OC NED 86.3 Alive
13 VU283 2004-11-24-CHC80-Chung-HumanX3P-Rep1.CEL 47 M s->xrt/chemo T2N2aM0 OP NED 57.6 Alive
14 VU284 2005-01-27-CHC110-Chung-HumanX3P-Rep1.CEL 63 M s->xrt/chemo T4N1M0 OP NED 11.6 DOC
15 VU285 2005-01-27-CHC109-Chung-HumanX3P-Rep1.CEL 60 M s->xrt T1N2bM0 OC NED 82.5 Alive
16 VA291 2005-01-14-CHC96-Chung-HumanX3P-Rep1.CEL 47 M s->xrt/chemo T3N2bM0 OP NED 9.5 DOC
17 VU99-6018 2005-03-16-CHC150-Chung-HumanX3P-Rep1.CEL 74 M s T2N0M0 OC REC 25.1 Alive

Total number of rows: 40

Table truncated, full table size 3 Kbytes.




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