Abstract

Most human genes produce multiple mRNA isoforms through alternative splicing. However, the biological relevance of most splice variants remains unclear. In this study, we evaluated the functional impact of alternative splicing in cancer cells. We modulated the splicing pattern of 41 cancer-associated splicing events and scored the effects on cell growth, viability and apoptosis, identifying three isoforms essential for cell survival. Specifically, changing the splicing pattern of the spleen tyrosine kinase gene (SYK) impaired cell-cycle progression and anchorage-independent growth. Notably, exposure of cancer cells to epithelial growth factor modulated the SYK splicing pattern to promote the pro-survival isoform that is associated with cancer tissues in vivo. The data suggest that splicing of selected genes is specifically modified during tumor development to allow the expression of isoforms that promote cancer cell survival.

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Acknowledgements

We are indebted to C. Rancourt (Département de Microbiologie, Université de Sherbrooke) for providing cell lines and help in the initial setup phase of the project and to B. Lamontagne and L. Bergeron Jr. for assay setup and help with troubleshooting. We thank the Réseau de Recherche sur le Cancer (Fonds de la Recherche en Santé du Québec; FRSQ) tissue bank for ovarian tumor tissues and L. Volkov for help with flow cytometry. This work was funded by Genome Canada/Génome Québec and National Cancer Institute of Canada grant no. 700529. B.C. is the Canada Research Chair in Functional Genomics. J.-P.P. is the Canada Research Chair on Genomics and Catalytic RNA. S.A.E. is a Chercheur National of the FRSQ.

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Affiliations

  1. Laboratoire de Génomique Fonctionnelle, Université de Sherbrooke, Sherbrooke, Québec, Canada.

    • Panagiotis Prinos
    • , Daniel Garneau
    • , Jean-François Lucier
    • , Daniel Gendron
    • , Sonia Couture
    • , Marianne Boivin
    • , Jean-Philippe Brosseau
    • , Elvy Lapointe
    • , Philippe Thibault
    • , Mathieu Durand
    • , Karine Tremblay
    • , Julien Gervais-Bird
    • , Hanad Nwilati
    • , Roscoe Klinck
    • , Benoit Chabot
    •  & Sherif Abou Elela
  2. Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada.

    • Jean-Philippe Brosseau
    •  & Jean-Pierre Perreault
  3. Département de Microbiologie et d'Infectiologie, Université de Sherbrooke, Sherbrooke, Québec, Canada.

    • Roscoe Klinck
    • , Benoit Chabot
    • , Raymund J Wellinger
    •  & Sherif Abou Elela

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Contributions

D. Garneau, M.B., D. Gendron., S.C., J.-P.B., E.L. and M.D. carried out experiments and analyzed data and J.-F.L., P.T. and J.G.-B. analyzed data and prepared the figures. J.-F.L. developed the ISI design program and the FASE statistics and bioinformatics analysis tools. J.-P.B., K.T., E.L. and P.T. developed the qPCR procedures used to evaluate ISI impact on splicing. H.N. did the histopathological review of tissue specimens. P.P., K.T., R.K., J.-P.P., B.C., R.J.W. and S.A.E. designed experiments, discussed data and participated in the writing of the paper. P.P. and K.T. supervised experiments and analyzed data. P.P. and S.A.E. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Sherif Abou Elela.

Supplementary information

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    Supplementary Text and Figures

    Supplementary Figures 1–9, Supplementary Tables 1 and 3, and Supplementary Methods

Excel files

  1. 1.

    Supplementary Table 2

    Primary FASE screen results. The results of the primary screen are shown, and the numbers of ISIs that are above the Z-score cut-off (>3) are indicated for each gene and each assay separately. Only ASEs with more than two positive ISIs per assay were retained for the validation phase (phase 2).

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DOI

https://doi.org/10.1038/nsmb.2040

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