Open Access Research article

Transcribed-ultra conserved region expression is associated with outcome in high-risk neuroblastoma

Paola Scaruffi1*, Sara Stigliani1, Stefano Moretti2, Simona Coco1, Carla De Vecchi1, Francesca Valdora3, Alberto Garaventa4, Stefano Bonassi5 and Gian Paolo Tonini1

Author Affiliations

1 Translational Paediatric Oncology, National Cancer Research Institute (IST), Largo R. Benzi 10, Genoa, 16132, Italy

2 Molecular Epidemiology, National Cancer Research Institute (IST), Largo R. Benzi 10, Genoa, 16132, Italy

3 Department of Oncology and Genetics (DOBIG), University of Genoa, Largo R. Benzi 10, Genoa, 16132, Italy

4 Department of Hematology-Oncology, Gaslini Institute, Largo G. Gaslini 5, Genoa, 16148, Italy

5 Clinical and Molecular Epidemiology, IRCCS San Raffaele Pisana, Via della Pisana 235, Roma, 00163, Italy

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BMC Cancer 2009, 9:441  doi:10.1186/1471-2407-9-441

Published: 15 December 2009

Abstract

Background

Neuroblastoma is the most common, pediatric, extra-cranial, malignant solid tumor. Despite multimodal therapeutic protocols, outcome for children with a high-risk clinical phenotype remains poor, with long-term survival still less than 40%. Hereby, we evaluated the potential of non-coding RNA expression to predict outcome in high-risk, stage 4 neuroblastoma.

Methods

We analyzed expression of 481 Ultra Conserved Regions (UCRs) by reverse transcription-quantitative real-time PCR and of 723 microRNAs by microarrays in 34 high-risk, stage 4 neuroblastoma patients.

Results

First, the comparison of 8 short- versus 12 long-term survivors showed that 54 UCRs were significantly (P < 0.0491) over-expressed in the former group. For 48 Ultra Conserved Region (UCRs) the expression levels above the cut-off values defined by ROC curves were strongly associated with good-outcome (OS: 0.0001 <P < 0.0185, EFS: 0.0001 <P < 0.0491). Then we tested the Transcribed-UCR (T-UCR) threshold risk-prediction model on an independent cohort of 14 patients. The expression profile of 28 T-UCRs was significantly associated to prognosis and at least 15 up-regulated T-UCRs are needed to discriminate (P < 0.0001) short- from long-survivors at the highest sensitivity and specificity (94.12%). We also identified a signature of 13 microRNAs differently expressed between long- and short-surviving patients. The comparative analysis of the two classes of non-coding RNAs disclosed that 9 T-UCRs display their expression level that are inversely correlated with expression of 5 complementary microRNAs of the signature, indicating a negative regulation of T-UCRs by direct interaction with microRNAs. Moreover, 4 microRNAs down-regulated in tumors of long-survivors target 3 genes implicated in neuronal differentiation, that are known to be over-expressed in low-risk tumors.

Conclusions

Our pilot study suggests that a deregulation of the microRNA/T-UCR network may play an important role in the pathogenesis of neuroblastoma. After further validation on a larger independent set of samples, such findings may be applied as the first T-UCR prognostic signature for high-risk neuroblastoma patients.