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DNA repair processes are critical mediators of p53-dependent tumor suppression

Nature Medicine volume 24, pages 947–953 (2018)Cite this article

Abstract

It has long been assumed that p53 suppresses tumor development through induction of apoptosis, possibly with contributions by cell cycle arrest and cell senescence1,2. However, combined deficiency in these three processes does not result in spontaneous tumor formation as observed upon loss of p53, suggesting the existence of additional mechanisms that are critical mediators of p53-dependent tumor suppression function3,4,5. To define such mechanisms, we performed in vivo shRNA screens targeting p53-regulated genes in sensitized genetic backgrounds. We found that knockdown of Zmat3, Ctsf and Cav1, promoted lymphoma/leukemia development only when PUMA and p21, the critical effectors of p53-driven apoptosis, cell cycle arrest and senescence, were also absent. Notably, loss of the DNA repair gene Mlh1 caused lymphoma in a wild-type background, and its enforced expression was able to delay tumor development driven by loss of p53. Further examination of direct p53 target genes implicated in DNA repair showed that knockdown of Mlh1, Msh2, Rnf144b, Cav1 and Ddit4 accelerated MYC-driven lymphoma development to a similar extent as knockdown of p53. Collectively, these findings demonstrate that extensive functional overlap of several p53-regulated processes safeguards against cancer and that coordination of DNA repair appears to be an important process by which p53 suppresses tumor development.

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Fig. 1: In vivo shRNA library screening to identify critical effectors of p53-mediated tumor suppression.
Fig. 2: Validation of candidate tumor suppressor genes.
Fig. 3: MLH1 is a critical contributor to p53-mediated tumor suppression.
Fig. 4: Several p53-regulated DNA repair genes function as tumor suppressor genes.

References

  1. Cheok, C. F., Verma, C. S., Baselga, J. & Lane, D. P. Translating p53 into the clinic. Nat. Rev. Clin. Oncol. 8, 25–37 (2011).

    Article  PubMed  CAS  Google Scholar 

  2. Chan, T. A., Hwang, P. M., Hermeking, H., Kinzler, K. W. & Vogelstein, B. Cooperative effects of genes controlling the G2/M checkpoint. Genes Dev. 14, 1584–1588 (2000).

    PubMed  PubMed Central  CAS  Google Scholar 

  3. Brady, C. A. et al. Distinct p53 transcriptional programs dictate acute DNA-damage responses and tumor suppression. Cell 145, 571–583 (2011).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  4. Li, T. et al. Tumor suppression in the absence of p53-mediated cell-cycle arrest, apoptosis, and senescence. Cell 149, 1269–1283 (2012).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  5. Valente, L. J. et al. p53 efficiently suppresses tumor development in the complete absence of its cell-cycle inhibitory and proapoptotic effectors p21, Puma, and Noxa. Cell Rep. 3, 1339–1345 (2013).

    Article  PubMed  CAS  Google Scholar 

  6. Muller, P. A. & Vousden, K. H. p53 mutations in cancer. Nat. Cell Biol. 15, 2–8 (2013).

    Article  PubMed  CAS  Google Scholar 

  7. Vogelstein, B., Lane, D. & Levine, A. J. Surfing the p53 network. Nature 408, 307–310 (2000).

    Article  PubMed  CAS  Google Scholar 

  8. Lowe, S. W. et al. p53 status and the efficacy of cancer therapy in vivo. Science 266, 807–810 (1994).

    Article  PubMed  CAS  Google Scholar 

  9. Donehower, L. A. et al. Mice deficient for p53 are developmentally normal but are susceptible to spontaneous tumors. Nature 356, 215–221 (1992).

    Article  PubMed  CAS  Google Scholar 

  10. Jacks, T. et al. Tumor spectrum analysis in p53-mutant mice. Curr. Biol. 4, 1–7 (1994).

    Article  PubMed  CAS  Google Scholar 

  11. Brady, C. A. & Attardi, L. D. p53 at a glance. J. Cell. Sci. 123, 2527–2532 (2010).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  12. Kenzelmann Broz, D. et al. Global genomic profiling reveals an extensive p53-regulated autophagy program contributing to key p53 responses. Genes Dev. 27, 1016–1031 (2013).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  13. Jeffers, J. R. et al. Puma is an essential mediator of p53-dependent and -independent apoptotic pathways. Cancer Cell 4, 321–328 (2003).

    Article  PubMed  CAS  Google Scholar 

  14. Villunger, A. et al. p53- and drug-induced apoptotic responses mediated by BH3-only proteins puma and noxa. Science 302, 1036–1038 (2003).

    Article  PubMed  CAS  Google Scholar 

  15. Deng, C., Zhang, P., Harper, J. W., Elledge, S. J. & Leder, P. Mice lacking p21CIP1/WAF1 undergo normal development, but are defective in G1 checkpoint control. Cell 82, 675–684 (1995).

    Article  PubMed  CAS  Google Scholar 

  16. Michalak, E. M. et al. Puma and to a lesser extent Noxa are suppressors of Myc-induced lymphomagenesis. Cell Death Differ. 16, 684–696 (2009).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  17. Valente, L. J., Grabow, S., Vandenberg, C. J., Strasser, A. & Janic, A. Combined loss of PUMA and p21 accelerates c-MYC-driven lymphoma development considerably less than loss of one allele of p53. Oncogene (2015).

  18. Riley, T., Sontag, E., Chen, P. & Levine, A. Transcriptional control of human p53-regulated genes. Nat. Rev. Mol. Cell Biol. 9, 402–412 (2008).

    Article  PubMed  CAS  Google Scholar 

  19. Lee, K., Tosti, E. & Edelmann, W. Mouse models of DNA mismatch repair in cancer research. DNA Repair (Amst) 38, 140–146 (2016).

    Article  CAS  Google Scholar 

  20. Zhu, H. et al. Involvement of Caveolin-1 in repair of DNA damage through both homologous recombination and non-homologous end joining. PLoS ONE 5, e12055 (2010).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  21. Razani, B. et al. Caveolin-1 null mice are viable but show evidence of hyperproliferative and vascular abnormalities. J. Biol. Chem. 276, 38121–38138 (2001).

    Article  PubMed  CAS  Google Scholar 

  22. Bersani, C., Xu, L. D., Vilborg, A., Lui, W. O. & Wiman, K. G. Wig-1 regulates cell cycle arrest and cell death through the p53 targets FAS and 14-3-3sigma. Oncogene 33, 4407–4417 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  23. Harfe, B. D. & Jinks-Robertson, S. DNA mismatch repair and genetic instability. Annu. Rev. Genet. 34, 359–399 (2000).

    Article  PubMed  CAS  Google Scholar 

  24. Malkin, D. et al. Germ line p53 mutations in a familial syndrome of breast cancer, sarcomas, and other neoplasms. Science 250, 1233–1238 (1990).

    Article  PubMed  CAS  Google Scholar 

  25. Schneider, K., Zelley, K., Nichols, K. E. & Garber, J. Li-Fraumeni Syndrome (GeneReviews, Seattle, WA, USA, 1999 [updated 2013]).

  26. Sengupta, S. & Harris, C. C. p53: traffic cop at the crossroads of DNA repair and recombination. Nat. Rev. Mol. Cell Biol. 6, 44–55 (2005).

    Article  PubMed  CAS  Google Scholar 

  27. Lane, D. P. p53, guardian of the genome. Nature 358, 15–16 (1992).

    Article  PubMed  CAS  Google Scholar 

  28. Dudgeon, C. et al. The evolution of thymic lymphomas in p53 knockout mice. Genes Dev. 28, 2613–2620 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  29. Sofer, A., Lei, K., Johannessen, C. M. & Ellisen, L. W. Regulation of mTOR and cell growth in response to energy stress by REDD1. Mol. Cell Biol. 25, 5834–5845 (2005).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  30. Williams, A. B. & Schumacher, B. p53 in the DNA-damage-repair process. Cold Spring Harb. Perspect. Med. 6, a026070 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  31. Dickins, R. A. et al. Probing tumor phenotypes using stable and regulated synthetic microRNA precursors. Nat. Genet. 37, 1289–1295 (2005).

    Article  PubMed  CAS  Google Scholar 

  32. Aubrey, B. J. et al. An inducible lentiviral guide RNA platform enables the identification of tumor-essential genes and tumor-promoting mutations in vivo. Cell Rep. 10, 1422–1432 (2015).

    Article  PubMed  CAS  Google Scholar 

  33. Wu, X. et al. Dimerization of MLH1 and PMS2 limits nuclear localization of MutL. Mol. Cell. Biol. 23, 3320–3328 (2003).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  34. Lois, C., Hong, E. J., Pease, S., Brown, E. J. & Baltimore, D. Germline transmission and tissue-specific expression of transgenes delivered by lentiviral vectors. Science 295, 868–872 (2002).

    Article  PubMed  CAS  Google Scholar 

  35. Herold, M. J., van den Brandt, J., Seibler, J. & Reichardt, H. M. Inducible and reversible gene silencing by stable integration of an shRNA-encoding lentivirus in transgenic rats. Proc. Natl Acad. Sci. USA 105, 18507–18512 (2008).

    Article  PubMed  Google Scholar 

  36. Strasser, A. et al. Enforced BCL2 expression in B-lymphoid cells prolongs antibody responses and elicits autoimmune disease. Proc. Natl Acad. Sci. USA 88, 8661–8665 (1991).

    Article  PubMed  CAS  Google Scholar 

  37. Dimri, G. P. et al. A biomarker that identifies senescent human cells in culture and in aging skin in vivo. Proc. Natl Acad. Sci. USA 92, 9363–9367 (1995).

    Article  PubMed  CAS  Google Scholar 

  38. Wang, H. et al. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153, 910–918 (2013).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  39. Kueh, A. J. et al. An update on using CRISPR/Cas9 in the one-cell stage mouse embryo for generating complex mutant alleles. Cell Death Differ. 24, 1821–1822 (2017).

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  40. Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. https://arxiv.org/abs/1303.3997 (2013).

  41. Josephidou, M., Lynch, A. G. & Tavaré, S. multiSNV: a probabilistic approach for improving detection of somatic point mutations from multiple related tumor samples. Nucleic Acids Res. 43, e61–e61 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  42. Derrien, T. et al. Fast computation and applications of genome mappability. PLoS ONE 7, e30377 (2012).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  43. Obenchain, V. et al. VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants. Bioinformatics 30, 2076–2078 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  44. Willems, T. et al. Genome-wide profiling of heritable and de novo STR variations. Nat. Meth. 14, 590–592 (2017).

    Article  CAS  Google Scholar 

  45. Scheinin, I. et al. DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Genome Res. 24, 2022–2032 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  46. Cameron, D. L. et al. GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly. bioRxiv 110387 (2017).

  47. Cameron, D. L. et al. GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly. Genome Res. 27, 2050–2060 (2017).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  48. Yin, T., Cook, D. & Lawrence, M. ggbio: an R package for extending the grammar of graphics for genomic data. Genome Biol. 13, R77 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank S. Lowe, A. Lujambio, A. Ventura and C. Concepcion for the p53 target gene shRNA library and for discussions; M. Ritchie, W. Shi, Y. Liao for data analysis, J.M. Adams, P. Bouillet, S. Cory, K. Rajewsky and A. Villunger for gifts of mice and for discussions. This work was supported by postdoctoral fellowships from the Leukemia & Lymphoma Society of America, Marie Curie Actions and Beatriu de Pinos, and Lady Tata Memorial Trust to A.J. and by grants from Cancer Australia and Cure Cancer Australia Foundation (grant no. 1067571), the National Health and Medical Research Council (NHMRC; program grant no. 1016701, NHMRC Senior Principal Research Fellow (SPRF) Fellowship 1020363 to A.S.), and the Leukemia & Lymphoma Society of America (Specialized Center of Research (SCOR) grant no. 7001-13), Australian Phenomics Network and a CCV Venture Grant. This work was made possible by operational infrastructure grants through the Australian Government Independent Medical Research Institutes Infrastructure Support Scheme (IRIISS) and the Victorian State Government Operational Infrastructure Support (OIS).

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Author notes

  1. These authors contributed equally: Liz J. Valente, Matthew J. Wakefield.

  2. These authors jointly supervised this work: Liam O’Connor, Andreas Strasser, Marco J. Herold.

Authors and Affiliations

  1. Molecular Genetics of Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia

    Ana Janic, Liz J. Valente, Matthew J. Wakefield, Leon Di Stefano, Liz Milla, Stephen Wilcox, Haoyu Yang, Lin Tai, Cassandra J. Vandenberg, Andrew J. Kueh, Shinsuke Mizutani, Margs S. Brennan, Robyn L. Schenk, Lisa M. Lindqvist, Anthony T. Papenfuss, Liam O’Connor, Andreas Strasser & Marco J. Herold

  2. Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia

    Ana Janic, Liz J. Valente, Liz Milla, Stephen Wilcox, Haoyu Yang, Cassandra J. Vandenberg, Andrew J. Kueh, Shinsuke Mizutani, Margs S. Brennan, Robyn L. Schenk, Lisa M. Lindqvist, Anthony T. Papenfuss, Liam O’Connor, Andreas Strasser & Marco J. Herold

  3. Stanford University School of Medicine, Division of Radiation Oncology–Radiation and Cancer Biology, Stanford, CA, USA

    Liz J. Valente

  4. Melbourne Bioinformatics, University of Melbourne, Carlton, Victoria, Australia

    Matthew J. Wakefield

  5. School of Pharmaceutical Sciences, Tsinghua University, Beijing, China

    Haoyu Yang

  6. Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia

    Anthony T. Papenfuss

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Contributions

The experiments were conceived and designed by A.J., M.J.H., L.O. and A.S. Experiments were performed mainly by A.J. with help from L.J.V., H.Y., L.T., L.M., S.W., C.J.V., S.M., A.J.K., M.S.B., L.M.L. and R.L.S. Whole genome sequencing analysis was performed by L.D.S., M.J.W. and A.T.P. The paper was written by A.J., M.J.H., L.O. and A.S. with help from the other authors.

Corresponding author

Correspondence to Andreas Strasser.

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Supplementary Figures 1–20 and Supplementary Tables 2–4

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Supplementary Table 1

p53 gene targeted shRNA library

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Janic, A., Valente, L.J., Wakefield, M.J. et al. DNA repair processes are critical mediators of p53-dependent tumor suppression. Nat Med 24, 947–953 (2018). https://doi.org/10.1038/s41591-018-0043-5

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