Dataset Information

ALDH2, CCNE1 and SMAD3 are Potential Prognostic Markers for Upper Tract Urothelial Carcinoma Revealed by Massively Parallel Sequencing.

ABSTRACT: Purpose: upper tract urothelial carcinoma (UTUC) is the predominant subtype of the renal pelvis carcinoma but current knowledge about the molecular properties and prognostic markers is sparse. In this study, we examined the genome-wide mRNA expression spectrum of UTUC aiming to characterize the molecular basis of this cancer, and identify potential prognostic markers and thus facilitate the clinical practices. Experimental Design: we compared the whole mRNA expression spectrum of cancer and matched normal tissues in 10 patients with UTUC using massively parallel sequencing, thereafter the protein levels and prognostic roles of ALDH2, CCNE1 and SMAD3 were evaluated under an independent validation set comprising of 104 patients. Results: mRNA down-regulation of ALDH2 and up-regulation of SMAD3 and CCNE1 in UTUC were revealed by expression profiling. And low protein expression of ALDH2 was associated with an adverse outcome for patients (p < 0.0001). Whereas high CCNE1 and SMAD3 were associated with adverse clinical outcome (p < 0.0001). And multivariate analysis revealed that all these three molecular markers were independent prognostic predictors. Besides, compared to the pathological TNM classification, All ALDH2, CCNE1 and SMAD3 were more competent in identifying patient subgroup with high mortality risk, and the molecular markers were able to predict the survival difference in the patients of T2 and T3 subgroup (p < 0.001), which could not be achieved by TNM staging. Conclusions: This is the ﬁrst prospective study that characterizes genome-wide mRNA expression profile of UTUC. We revealed the prognostic significance of ALDH2, CCNE1 and SMAD3, and these molecular marker were more robust than TNM system in clinical outcome prediction.

ORGANISM(S): Homo sapiens

PROVIDER: GSE47702 | GEO | 2015/01/01

SECONDARY ACCESSION(S): PRJNA207338

REPOSITORIES: GEO

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Project description:TP53 mutations are a poor prognostic factor in breast cancers. This study sets out to identify the gene set that determine expression signature of the TP53 status (TP53 signature) and to correlate it with clinical outcome. Using comprehensive expression analysis and DNA sequencing of the TP53 gene in 38 Japanese breast cancer patients, we have isolated a gene set of 33 genes from differentially expressed genes in the learning set (n=26), depending on the TP53 status. Predictive accuracy of TP53 status by gene expression profile was 83.3% in the test set (n=12). As independent external datasets, two published datasets were introduced for validation of TP53 status prediction (251 Swedish samples) and survival analysis (both the Swedish and 295 Dutch samples). TP53 signature has the ability to predict recurrence-free survival (RFS) of 29 stage I and II Japanese breast cancers (log rank, P = 0.032), and RFS, overall survival of two independently published datasets (log rank, both P < 0.0001). Multivariate analysis has shown an independent and significant prognostic factor with a hazard ratio (HR) for recurrence and survival in two external datasets (P < 0.0001). The TP53 signature is also a strong prognostic factor in the subgroups: estrogen-receptor positive, lymph node (LN) positive and negative, intermediate/high risk in St. Gallen criteria, and high risk in National Cancer Institute (NCI) criteria (log rank, P < 0.0001). TP53 signature is a reliable and independent predictor of the outcome of disease in operated breast cancer. Experiment Overall Design: Microarray hybridizations (Agilent: Whole Human Genome Oligo Microarray; 41k unique probe) were carried out with 1Î¼g Cy3 labeled cRNA and 1 Î¼g Cy5 labeled cRNA, both prepared from each sample and reference pool, respectively. Experiment Overall Design: Fluorescent intensities of scanned images were quantified by ArrayVision Ver.8 rev.4 (Imaging research). Experiment Overall Design: The gene expression data was quantified and analyzed by GeneSpring 6.2 (Silicon Genetics). To identify the TP53 status predictor gene set, a Wilcoxon rank sum test along with Benjamini and Hochberg false discovery rate (FDR) was used.

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ALDH2, CCNE1 and SMAD3 are Potential Prognostic Markers for Upper Tract Urothelial Carcinoma Revealed by Massively Parallel Sequencing.

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