Transcriptomics

Dataset Information

27

Gene expression analysis of relapse and no-relapse Wilms tumor


ABSTRACT: Wilms tumor (WT), the commonest renal tumor of the childhood, is originated from pluripotent metanephric blastemal cells resulting in tumors with triphasic histology, composed by blastemal, epithelial, and stromal cells. Histological subtype and tumor stage have long been recognized as important prognostic factors and used for the current therapeutic approach with blastema considered as the component with the highest clinical impact. Current clinical and molecular research is directed toward identifying prognostic factors for both purposes, definition of the minimal or intense required therapy for successful treatment of children with low or high risk of relapse, respectively. In this study, to identify molecular prognostic markers predictive of tumor relapse, samples from 26 advanced (Stage III or IV) blastemal WT, whose patients presented (13 samples) or did not present (13 samples) relapse, were interrogated by 4,608 human genes immobilized in a customized cDNA platform. This analysis revealed a set of 69 differentially expressed genes, where the nine top genes were evaluated by qRT-PCR in the initial WT samples. TSPAN3, NCOA6, CDO1, MPP2 and MCM2 were technically confirmed showing down-regulation in relapse WT. TSPAN3 and NCOA6 were validated in an independent sample group. Gene trios containing these two genes combined with one of the remaining three reported a reasonable capability of discriminating relapse and no-relapse WT. Negative protein expression of MCM2 and NCOA6 was observed in around 62% and 72% of 34 independent stage III and IV WT patients, respectively without association with relapse. However, a significant association between MCM2 negative staining and chemotherapy as first treatment was observed suggesting that MCM2 protein expression is implicated anyhow with chemotherapy treatment in WT. Twenty-six blastemal-enriched advanced stage (III or IV) WT samples from sporadic and favorable histology WT were received from Children Oncology Group (COG) and used were used for microarray experiments, from which 13 samples were from patients without relapse in 5 years of follow up. Tumors were taken from primary nephrectomy at the time of initial diagnosis. Blastemal histological component was isolated following protocol described in Maschietto et al. (2008). Only samples with >80% of blastemal cells were used. Total RNA was isolated using TRIzol (Sigma) according to manufacturer´s instructions. RNA quantity and integrity was assessed by spectrophotometry (Nanodrop) and microfluidics-based electrophoresis (Agilent 2100 Bioanalyzer, Agilent), respectively, selecting only RNA samples with OD around 2.0 and RIN>5.0. A two-round RNA amplification procedure (Gomes et al. 2003) was carried out for all samples. Labeled cDNA was generated in a reverse transcriptase reaction using 4 ug of amplified RNA (aRNA), random hexamer primer (Invitrogen Life Technologies, Carlsbad, CA), Alexa-3 or 5-labeled dCTP (Amersham, Biosciences) and IMPROM (PROMEGA) using oligo-dT7(24), following manufacture recommendations. Five µg of test and reference cDNA reverse color Alexa-labeled aRNA targets were competitively hybridized against the cDNA probes in a customized cDNA platform with 4,608 ORESTES representing human genes. Dye-swap was performed for each sample as control for dye bias and used as replicate. Pre-hybridization and hybridization were performed as described (Maschietto et al. 2008). A pool of RNAs obtained from 15 distinct human cell lines as was used as reference. Signal intensities capture and analysis were performed as described in Maschietto et al (2008).

ORGANISM(S): Homo sapiens  

SUBMITTER: Mariana Maschietto   

PROVIDER: E-GEOD-22696 | ArrayExpress| 2014-05-01

SECONDARY ACCESSION(S): GSE22696PRJNA128307

REPOSITORIES: GEO, ArrayExpress

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