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Transcriptome profiling of UPF3B/NMD-deficient lymphoblastoid cells from patients with various forms of intellectual disability

Molecular Psychiatry volume 17, pages 1103–1115 (2012)Cite this article

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Abstract

The nonsense-mediated mRNA decay (NMD) pathway was originally discovered by virtue of its ability to rapidly degrade aberrant mRNAs with premature termination codons. More recently, it was shown that NMD also directly regulates subsets of normal transcripts, suggesting that NMD has roles in normal biological processes. Indeed, several NMD factors have been shown to regulate neurological events (for example, neurogenesis and synaptic plasticity) in numerous vertebrate species. In man, mutations in the NMD factor gene UPF3B, which disrupts a branch of the NMD pathway, cause various forms of intellectual disability (ID). Using Epstein Barr virus—immortalized B cells, also known as lymphoblastoid cell lines (LCLs), from ID patients that have loss-of-function mutations in UPF3B, we investigated the genome-wide consequences of compromised NMD and the role of NMD in neuronal development and function. We found that ∼5% of the human transcriptome is impacted in UPF3B patients. The UPF3B paralog, UPF3A, is stabilized in all UPF3B patients, and partially compensates for the loss of UPF3B function. Interestingly, UPF3A protein, but not mRNA, was stabilised in a quantitative manner that inversely correlated with the severity of patients' phenotype. This suggested that the ability to stabilize the UPF3A protein is a crucial modifier of the neurological symptoms due to loss of UPF3B. We also identified ARHGAP24, which encodes a GTPase-activating protein, as a canonical target of NMD, and we provide evidence that deregulation of this gene inhibits axon and dendrite outgrowth and branching. Our results demonstrate that the UPF3B-dependent NMD pathway is a major regulator of the transcriptome and that its targets have important roles in neuronal cells.

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Acknowledgements

We thank the members of the families studied for participation and Brigitte Jauffrion and Lucianne Vandeleur for help with cell culture. This work was supported by grants from the Australian NH&MRC Project Grant 453457 to JoG, and the Women's and Children's Hospital Foundation Grant to LJ and JoG. JoG is supported by NH&MRC Principal Research Fellowship. LSN's PhD scholarship was supported by the MS McLeod Foundation.

Author contributions: LSN performed most of the data analysis; LJ performed the overexpression of ARHGAP24 in mouse primary hippocampal neurons; CS performed the overexpression of ARHGAP24 in mouse PC12 cell line; WC, LH and MFW contributed the microarray and reverse-transcriptase quantitative PCR data of NMD knockdown in HeLa cells; LH performed the RNAi knockdown of UPF1, UPF2 and SMG1 in HeLa cells; SS performed the in situ hybridization of ARHGAP24 in human brain sample; CH and JeG generated the antibody against ARHGAP24 isoform 1 and the ARHGAP24 isoform 1 clone; FL, MR, AH, MF, JR, AKS, LY, AAM and JLR contributed with patient material or LCL lines for this work; MC provided advice on the data analysis; This project was designed and supervised by JoG; The paper was written by LSN, LJ and JoG, with advice from MFW.

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Authors and Affiliations

  1. Department of Paediatrics, University of Adelaide, Adelaide, SA, Australia

    L S Nguyen, C Shoubridge & J Gecz

  2. Department of Genetic Medicine, SA Pathology, Adelaide, SA, Australia

    L S Nguyen, L Jolly, C Shoubridge, M A Corbett & J Gecz

  3. Department of Bioinformatics and Computational Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA

    W K Chan

  4. Department of Reproductive Medicine, University of California, San Diego, CA, USA

    L Huang & M F Wilkinson

  5. INSERM, U930, Tours, France

    F Laumonnier & M Raynaud

  6. CNRS, ERL3106, Tours, France

    F Laumonnier

  7. University Francois-Rabelais, UMR ‘Imaging and Brain’, Tours, France

    F Laumonnier & M Raynaud

  8. CHRU de Tours, Service de Genetique, Tours, France

    M Raynaud

  9. GOLD Service, Hunter Genetics, Newcastle, Australia

    A Hackett & M Field

  10. J.C. Self Research Institute, Greenwood Genetic Centre, Greenwood, SC, USA

    J Rodriguez & A K Srivastava

  11. Child Psychiatry Branch, National Institute of Mental Health, Bethesda, MD, USA

    Y Lee, R Long, A M Addington & J L Rapoport

  12. Human Developmental Biology Resource, Neural Development Unit, UCL Institute of Child Health, London, UK

    S Suren

  13. Department of Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia

    C N Hahn

  14. Centenary Institute of Cancer Medicine & Cell Biology, University of Sydney, NSW, Australia

    J Gamble

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  1. L S Nguyen
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  2. L Jolly
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Nguyen, L., Jolly, L., Shoubridge, C. et al. Transcriptome profiling of UPF3B/NMD-deficient lymphoblastoid cells from patients with various forms of intellectual disability. Mol Psychiatry 17, 1103–1115 (2012). https://doi.org/10.1038/mp.2011.163

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