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The deubiquitinase USP9X suppresses pancreatic ductal adenocarcinoma

A Corrigendum to this article was published on 30 January 2013

Abstract

Pancreatic ductal adenocarcinoma (PDA) remains a lethal malignancy despite much progress concerning its molecular characterization. PDA tumours harbour four signature somatic mutations1,2,3,4 in addition to numerous lower frequency genetic events of uncertain significance5. Here we use Sleeping Beauty (SB) transposon-mediated insertional mutagenesis6,7 in a mouse model of pancreatic ductal preneoplasia8 to identify genes that cooperate with oncogenic KrasG12D to accelerate tumorigenesis and promote progression. Our screen revealed new candidate genes for PDA and confirmed the importance of many genes and pathways previously implicated in human PDA. The most commonly mutated gene was the X-linked deubiquitinase Usp9x, which was inactivated in over 50% of the tumours. Although previous work had attributed a pro-survival role to USP9X in human neoplasia9, we found instead that loss of Usp9x enhances transformation and protects pancreatic cancer cells from anoikis. Clinically, low USP9X protein and messenger RNA expression in PDA correlates with poor survival after surgery, and USP9X levels are inversely associated with metastatic burden in advanced disease. Furthermore, chromatin modulation with trichostatin A or 5-aza-2′-deoxycytidine elevates USP9X expression in human PDA cell lines, indicating a clinical approach for certain patients. The conditional deletion of Usp9x cooperated with KrasG12D to accelerate pancreatic tumorigenesis in mice, validating their genetic interaction. We propose that USP9X is a major tumour suppressor gene with prognostic and therapeutic relevance in PDA.

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Figure 1: Transposon mutagenesis accelerates murine PDA and targets Usp9x.
Figure 2: Usp9x regulates PDA cellular transformation and Itch.
Figure 3: USP9X loss promotes PDA.

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Gene Expression Omnibus

Data deposits

The GEO accession number for the ICGC/APGI gene expression data is GSE36924.

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Acknowledgements

We thank P. Labosky for assistance in generating the Rosa26-LSL-SB13 mouse; B. Bhagavan for pathology consultation; M. Tsao for providing the HPDE cell line; and N. Copeland and K. Mann for sharing pre-published information. We thank A. Gopinathan, H. Tiriac, D. Engle, D. Chan, F. Connor, S. Derkits and other members of the Tuveson laboratory for assistance and advice, and the animal care staff and histology core at CRI, and The University of Minnesota’s Mouse Genetics Laboratory. This research was supported by the University of Cambridge and Cancer Research UK, The Li Ka Shing Foundation and Hutchison Whampoa Limited, the NIHR Cambridge Biomedical Research Centre, and the NIH (2P50CA101955 SPORE grant to D.A.T., D.A.L. and C.A.I.-D.; grants CA62924, CA128920 and CA106610 to C.A.I.-D.; P50CA62924 SPORE grant to R.H.H. and C.A.I.-D.; and CA122183 to L.S.C.). D.J.A. is supported by Cancer Research UK and the Wellcome Trust. L.v.d.W. is supported by the Kay Kendall Leukemia Fund. C.P. is supported by Wilhelm Sander Stiftung (2009.039.1) and Deutsche Forschungsgemeinschaft (PI 341/5-1). A.V.B., D.K.C., S.M.G. and the APGI investigators are funded by the University of Verona and Italian Ministry of University and Research (FIRB RBAP10AHJB); the National Health and Medical research Council of Australia (NHMRC); Queensland Government; Cancer Council NSW; Australian Cancer Research Foundation; Cancer Institute NSW; The Avner Nahmani Pancreatic Cancer Research Foundation; and the R.T. Hall Trust. S.A.W. was supported by the NHMRC. Additional support was obtained from Fundación Ibercaja (P.A.P.-M.).

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Contributions

P.A.P.-M. performed the majority of all experiments, designed experiments, analysed data, and wrote the manuscript. L.v.d.W. and J.A.B. performed in vitro experiments. S.S. and S.A.W. generated the conditional Usp9x mouse. L.S.C. provided the CAGGS-SB10 and T2/Onc mice. A.G.R., A.L.S., K.A.T.S., J.J.t.H., J.d.R. and L.F.A.W. conducted the CIS data analysis. G.K., R.G., D.A., P.R., T.K. and C.P. generated data from resected pancreatic tumours. Allen Li, R.H.H., R.M., S.K., J.Y., Ang Li, M.G. and C.A.I.-D. analysed human samples from autopsy series, and analysed mouse pathology and methylation studies. C.H., D.L.S. and R.K. sequenced PDA human samples from autopsy series. A.P.K. provided statistical analyses for the human PDA data sets. APGI, D.K.C., S.M.G. and A.V.B. generated and analysed data from ICGC/APGI (International Cancer Genome Consortium/Australian Pancreatic Cancer Genome Initiative). D.A.L. provided the CAGGS-SB10 and T2/Onc mice, and analysed data. D.J.A. and D.A.T. designed the study, analysed the data, and wrote the manuscript. All authors commented upon and edited the final manuscript.

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Correspondence to David J. Adams or David A. Tuveson.

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Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-19, Supplementary Tables 1 and 5-11, full legends for Tables 2-4 and an additional reference. (PDF 15995 kb)

Supplementary Table 2

This table shows candidate CIS genes in pancreas tumours from KCTSB13 mice. (XLS 264 kb)

Supplementary Table 3

This file contains Supplementary Tables 3a and 3b as BED files which list non-redundant insertions. (ZIP 1026 kb)

Supplementary Table 4

This table shows comparison of KCTSB13 CISs to prior work in human PDA. (XLS 228 kb)

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Pérez-Mancera, P., Rust, A., van der Weyden, L. et al. The deubiquitinase USP9X suppresses pancreatic ductal adenocarcinoma. Nature 486, 266–270 (2012). https://doi.org/10.1038/nature11114

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