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Verification of genes differentially expressed in neuroblastoma tumours: A study of potential tumour suppressor genes
Department of Clinical Genetics, Gothenburg University, Gothenburg, Sweden.
Department of Pathology, Lundberg Laboratory for Cancer Research, SU/Sahlgrenska, Gothenburg, Sweden.
Department of Clinical Genetics, Gothenburg University, Gothenburg, Sweden.
Department of Mathematical Statistics, Chalmers University of Technology, Gothenburg, Sweden.
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2009 (English)In: BMC Medical Genomics, ISSN 1755-8794, E-ISSN 1755-8794, Vol. 2, article id 53Article in journal (Refereed) Published
Abstract [en]

Background: One of the most striking features of the childhood malignancy neuroblastoma (NB) is its clinical heterogeneity. Although there is a great need for better clinical and biological markers to distinguish between tumours with different severity and to improve treatment, no clear-cut prognostic factors have been found. Also, no major NB tumour suppressor genes have been identified.

Methods: In this study we performed expression analysis by quantitative real-time PCR (QPCR) on primary NB tumours divided into two groups, of favourable and unfavourable outcome respectively. Candidate genes were selected on basis of lower expression in unfavourable tumour types compared to favourables in our microarray expression analysis. Selected genes were studied in two steps: (1) using TaqMan Low Density Arrays (TLDA) targeting 89 genes on a set of 12 NB tumour samples, and (2) 12 genes were selected from the TLDA analysis for verification using individual TaqMan assays in a new set of 13 NB tumour samples.

Results: By TLDA analysis, 81 out of 87 genes were found to be significantly differentially expressed between groups, of which 14 have previously been reported as having an altered gene expression in NB. In the second verification round, seven out of 12 transcripts showed significantly lower expression in unfavourable NB tumours, ATBF1, CACNA2D3, CNTNAP2, FUSIP1, GNB1, SLC35E2, and TFAP2B. The gene that showed the highest fold change in the TLDA analysis, POU4F2, was investigated for epigenetic changes (CpG methylation) and mutations in order to explore the cause of the differential expression. Moreover, the fragile site gene CNTNAP2 that showed the largest fold change in verification group 2 was investigated for structural aberrations by copy number analysis. However, the analyses of POU4F2 and CNTNAP2 showed no genetic alterations that could explain a lower expression in unfavourable NB tumours.

Conclusion: Through two steps of verification, seven transcripts were found to significantly discriminate between favourable and unfavourable NB tumours. Four of the transcripts, CACNA2D3, GNB1, SLC35E2, and TFAP2B, have been observed in previous microarray studies, and are in this study independently verified. Our results suggest these transcripts to be markers of malignancy, which could have a potential usefulness in the clinic. 

Place, publisher, year, edition, pages
BioMed Central, 2009. Vol. 2, article id 53
Keywords [en]
antineoplastic agent, transcription factor, transcription factor ATBF1, transcription factor CACNA2D3, transcription factor FUSIP1, transcription factor GNB1, transcription factor POU4F2, transcription factor SLC35E2, transcription factor TFAP2B, unclassified drug, article, cancer surgery, child, clinical article, controlled study, disease severity, epigenetics, gene expression, gene identification, gene mutation, gene number, genetic difference, human, infant, microarray analysis, multiple cycle treatment, neuroblastoma, nucleotide sequence, outcome assessment, preschool child, priority journal, prognosis, protein methylation, quantitative analysis, real time polymerase chain reaction, risk factor, Taqman low density arrays, tumor classification, tumor suppressor gene
National Category
Medical Genetics
Identifiers
URN: urn:nbn:se:hj:diva-39620DOI: 10.1186/1755-8794-2-53ISI: 000272814700001PubMedID: 19686582Scopus ID: 2-s2.0-70349251320OAI: oai:DiVA.org:hj-39620DiVA, id: diva2:1211807
Available from: 2018-05-31 Created: 2018-05-31 Last updated: 2018-05-31Bibliographically approved

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