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Open Access Research article

NMD inhibition fails to identify tumour suppressor genes in microsatellite stable gastric cancer cell lines

Tineke E Buffart1, Marianne Tijssen1, Jamila El-Bchiri2, Alex Duval2, Mark A van de Wiel13, Bauke Ylstra1, Gerrit A Meijer1 and Beatriz Carvalho14*

Author Affiliations

1 Dept Pathology, VU University Medical Center, Amsterdam, The Netherlands

2 INSERM U434, Hôpital Saint-Louis, Paris, France

3 Dept Mathematics, VU University Medical Center, Amsterdam, The Netherlands

4 IPATIMUP, Department of Pathology, Medical Faculty, Hospital de S. João, Porto, Portugal

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BMC Medical Genomics 2009, 2:39  doi:10.1186/1755-8794-2-39

Published: 29 June 2009

Abstract

Background

Gastric cancers frequently show chromosomal alterations which can cause activation of oncogenes, and/or inactivation of tumour suppressor genes. In gastric cancer several chromosomal regions are described to be frequently lost, but for most of the regions, no tumour suppressor genes have been identified yet. The present study aimed to identify tumour suppressor genes inactivated by nonsense mutation and deletion in gastric cancer by means of GINI (gene identification by nonsense mediated decay inhibition) and whole genome copy number analysis.

Methods

Two non-commercial gastric cancer cell lines, GP202 and IPA220, were transfected with siRNA directed against UPF1, to specifically inhibit the nonsense mediated decay (NMD) pathway, and with siRNA directed against non-specific siRNA duplexes (CVII) as a control. Microarray expression experiments were performed in triplicate on 4 × 44 K Agilent arrays by hybridizing RNA from UPF1-transfected cells against non-specific CVII-transfected cells. In addition, array CGH of the two cell lines was performed on 4 × 44K agilent arrays to obtain the DNA copy number profiles. Mutation analysis of GINI candidates was performed by sequencing.

Results

UPF1 expression was reduced for >70% and >80% in the GP202 and IPA220 gastric cancer cell lines, respectively. Integration of array CGH and microarray expression data provided a list of 134 and 50 candidate genes inactivated by nonsense mutation and deletion for GP202 and IPA220, respectively. We selected 12 candidate genes for mutation analysis. Of these, sequence analysis was performed on 11 genes. One gene, PLA2G4A, showed a silent mutation, and in two genes, CTSA and PTPRJ, missense mutations were detected. No nonsense mutations were detected in any of the 11 genes tested.

Conclusion

Although UPF1 was substantially repressed, thus resulting in the inhibition of the NMD system, we did not find genes inactivated by nonsense mutations. Our results show that the GINI strategy leads to a high number of false positives.