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p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity

Abstract

In a search for mediators of the p53 tumor suppressor pathway, which induces pleiotropic and often antagonistic cellular responses, we identified the long noncoding RNA (lncRNA) NEAT1. NEAT1 is an essential architectural component of paraspeckle nuclear bodies, whose pathophysiological relevance remains unclear. Activation of p53, pharmacologically or by oncogene-induced replication stress, stimulated the formation of paraspeckles in mouse and human cells. Silencing Neat1 expression in mice, which prevents paraspeckle formation, sensitized preneoplastic cells to DNA-damage-induced cell death and impaired skin tumorigenesis. We provide mechanistic evidence that NEAT1 promotes ATR signaling in response to replication stress and is thereby engaged in a negative feedback loop that attenuates oncogene-dependent activation of p53. NEAT1 targeting in established human cancer cell lines induced synthetic lethality with genotoxic chemotherapeutics, including PARP inhibitors, and nongenotoxic activation of p53. This study establishes a key genetic link between NEAT1 paraspeckles, p53 biology and tumorigenesis and identifies NEAT1 as a promising target to enhance sensitivity of cancer cells to both chemotherapy and p53 reactivation therapy.

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Figure 1: p53 induces NEAT1 expression and paraspeckle formation.
Figure 2: DNA damage induces NEAT1 paraspeckle formation.
Figure 3: Neat1 KO mice are resistant to chemically induced skin cancer formation.
Figure 4: Neat1 prevents accumulation of DNA damage and p53.
Figure 5: NEAT1 paraspeckles modulate ATR signaling and chemosensitivity.
Figure 6: Detection of NEAT1 paraspeckles in human cancers and correlation of NEAT1_2 levels with response to platinum-based therapy.

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Acknowledgements

We thank O. Van Goethem, G. Bervoets and S. Peeters for excellent technical assistance; E. Bonomi and M. Bugatti (Fondazione Beretta) for ISH analysis of human cancer samples; and S. Jackson for helpful comments on the manuscript and for imaging facility access. Imaging was done on a Nikon A1 confocal microscope acquired through a Hercules grant type 1 (AKUL/09/037) to W. Annaert. This work was supported by Interuniversitaire Attractiepolen (IUAP), an Institute for Science, Innovation and Technology (IWT) scholarship to C.A. and a Fund for Scientific Research Flanders (FWO) scholarship to L.S. W.V. is supported by Associazione Italiana per la Ricerca sul Cancro (AIRC, IG 15378) and by Ministero Salute (RF-2010-2315888).

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C.A., L.S. and J.B. designed and conducted experiments and acquired, analyzed and interpreted the data. M.L. performed DMBA and TPA treatments and monitored tumor development. A.V. and S.A. performed p53 ChIP-seq and RNA-seq experiments and data analysis. P.K. assessed DNA damage repair efficacy with bleomycin. B. Boeckx and D.L. analyzed expression data and constructed KM curves. E.R. and J.v.d.O. provided mouse and human pathology support. J.v.d.O. provided clinical samples. A.A.S., C.B. and E.L. designed research studies and contributed to interpretation of the data. G.L. and B. Beck provided reagents from mouse skin tumors. S.N. and T.H. provided Neat1 KO mice. W.V. performed the TMA. P.W.G.W. provided reagents and contributed to interpretation of the data. All authors read and edited the manuscript. J.-C.M. designed research studies and wrote the manuscript.

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Correspondence to Jean-Christophe Marine.

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Adriaens, C., Standaert, L., Barra, J. et al. p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity. Nat Med 22, 861–868 (2016). https://doi.org/10.1038/nm.4135

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