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Identifying candidate colon cancer tumor suppressor genes using inhibition of nonsense-mediated mRNA decay in colon cancer cells

Oncogene volume 26, pages 2873–2884 (2007)Cite this article

Abstract

Inhibition of the nonsense-mediated decay (NMD) mechanism in cells results in stabilization of transcripts carrying premature translation termination codons. A strategy referred to as gene identification by NMD inhibition (GINI) has been proposed to identify genes carrying nonsense mutations. Genes containing frameshift mutations in colon cancer cell line have been identified using a modified version of GINI. To increase the efficiency of identifying mutant genes using GINI, we have now further improved the strategy. In this approach, inhibition of NMD with emetine is complemented with inhibiting NMD by blocking the phosphorylation of the hUpf1 protein with caffeine. In addition, to enhance the GINI strategy, comparing mRNA level alterations produced by inhibiting transcription alone or inhibiting transcription together with NMD following caffeine pretreatment were used for the efficient identification of false positives produced as a result of stress response to NMD inhibition. To demonstrate the improved efficiency of this approach, we analysed colon cancer cell lines showing microsatellite instability. Bi-allelic inactivating mutations were found in the FXR1, SEC31L1, NCOR1, BAT3, PHF14, ZNF294, C19ORF5 genes as well as genes coding for proteins with yet unknown functions.

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Acknowledgements

This work was supported by grants Roswell Park Alliance Foundation grant, 1R01 CA109256-01 from the National Cancer Institute and PC030076 from the Prostate Program of the United States Army Department of Defense (Yurij Ionov) and in part by the RPCI Cancer Center Support Grant CA 16056 for all authors and NIH NSO54543 (John Cowell).

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  1. Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY, USA

    I Ivanov, K C Lo, L Hawthorn, J K Cowell & Y Ionov

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Correspondence to Y Ionov.

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Ivanov, I., Lo, K., Hawthorn, L. et al. Identifying candidate colon cancer tumor suppressor genes using inhibition of nonsense-mediated mRNA decay in colon cancer cells. Oncogene 26, 2873–2884 (2007). https://doi.org/10.1038/sj.onc.1210098

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