Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Interplay between oncogene-induced DNA damage response and heterochromatin in senescence and cancer

Abstract

Two major mechanisms have been causally implicated in the establishment of cellular senescence: the activation of the DNA damage response (DDR) pathway and the formation of senescence-associated heterochromatic foci (SAHF). Here we show that in human fibroblasts resistant to premature p16INK4a induction, SAHF are preferentially formed following oncogene activation but are not detected during replicative cellular senescence or on exposure to a variety of senescence-inducing stimuli. Oncogene-induced SAHF formation depends on DNA replication and ATR (ataxia telangiectasia and Rad3-related). Inactivation of ATM (ataxia telangiectasia mutated) or p53 allows the proliferation of oncogene-expressing cells that retain increased heterochromatin induction. In human cancers, levels of heterochromatin markers are higher than in normal tissues, and are independent of the proliferative index or stage of the tumours. Pharmacological and genetic perturbation of heterochromatin in oncogene-expressing cells increase DDR signalling and lead to apoptosis. In vivo, a histone deacetylase inhibitor (HDACi) causes heterochromatin relaxation, increased DDR, apoptosis and tumour regression. These results indicate that heterochromatin induced by oncogenic stress restrains DDR and suggest that the use of chromatin-modifying drugs in cancer therapies may benefit from the study of chromatin and DDR status of tumours.

This is a preview of subscription content

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: SAHF are preferentially formed on oncogene-induced senescence in human normal fibroblasts.
Figure 2: SAHF formation requires DNA replication and is dependent on ATR.
Figure 3: Increased heterochromatin in DDR-deficient oncogene-expressing cells is compatible with cellular proliferation.
Figure 4: E2F target genes are not repressed by heterochromatin induction in DDR-deficient oncogene-expressing cells.
Figure 5: Increased heterochromatin is retained in human tumours in vivo in different stages of cancer progression.
Figure 6: SAHF and DDR markers coexist in OIS cells but do not colocalize.
Figure 7: Heterochromatin induction restrains oncogene-induced DDR signalling.
Figure 8: Oncogene-induced heterochromatin formation prevents apoptosis by restraining oncogene-induced DDR signalling.

References

  1. 1

    Collado, M., Blasco, M. A. & Serrano, M. Cellular senescence in cancer and aging. Cell 130, 223–233 (2007).

    CAS  Article  Google Scholar 

  2. 2

    Campisi, J. & d'Adda di Fagagna, F. Cellular senescence: when bad things happen to good cells. Nat. Rev. Mol. Cell Biol. 8, 729–740 (2007).

    CAS  Article  Google Scholar 

  3. 3

    Adams, P. D. Healing and hurting: molecular mechanisms, functions and pathologies of cellular senescence. Mol. Cell 36, 2–14 (2009).

    CAS  Article  Google Scholar 

  4. 4

    d'Adda di Fagagna, F. et al. A DNA damage checkpoint response in telomere-initiated senescence. Nature 426, 194–198 (2003).

    CAS  Article  Google Scholar 

  5. 5

    Herbig, U., Jobling, W. A., Chen, B. P., Chen, D. J. & Sedivy, J. M. Telomere shortening triggers senescence of human cells through a pathway involving ATM, p53, and p21(CIP1), but not p16(INK4a). Mol. Cell 14, 501–513 (2004).

    CAS  Article  Google Scholar 

  6. 6

    Karlseder, J., Smogorzewska, A. & de Lange, T. Senescence induced by altered telomere state, not telomere loss. Science 295, 2446–2449 (2002).

    CAS  Article  Google Scholar 

  7. 7

    Schmitt, C. A. Senescence, apoptosis and therapy—cutting the lifelines of cancer. Nat. Rev. Cancer 3, 286–295 (2003).

    CAS  Article  Google Scholar 

  8. 8

    Serrano, M., Lin, A. W., McCurrach, M. E., Beach, D. & Lowe, S. W. Oncogenic ras provokes premature cell senescence associated with accumulation of p53 and p16INK4a. Cell 88, 593–602 (1997).

    CAS  Article  Google Scholar 

  9. 9

    Halazonetis, T. D., Gorgoulis, V. G. & Bartek, J. An oncogene-induced DNA damage model for cancer development. Science 319, 1352–1355 (2008).

    CAS  Article  Google Scholar 

  10. 10

    Michaloglou, C. et al. BRAFE600-associated senescence-like cell cycle arrest of human naevi. Nature 436, 720–724 (2005).

    CAS  Article  Google Scholar 

  11. 11

    Chen, Z. et al. Crucial role of p53-dependent cellular senescence in suppression of Pten-deficient tumorigenesis. Nature 436, 725–730 (2005).

    CAS  Article  Google Scholar 

  12. 12

    Braig, M. et al. Oncogene-induced senescence as an initial barrier in lymphoma development. Nature 436, 660–665 (2005).

    CAS  Article  Google Scholar 

  13. 13

    Collado, M. et al. Tumour biology: senescence in premalignant tumours. Nature 436, 642 (2005).

    CAS  Article  Google Scholar 

  14. 14

    Bartkova, J. et al. Oncogene-induced senescence is part of the tumorigenesis barrier imposed by DNA damage checkpoints. Nature 444, 633–637 (2006).

    CAS  Article  Google Scholar 

  15. 15

    Denchi, E. L., Attwooll, C., Pasini, D. & Helin, K. Deregulated E2F activity induces hyperplasia and senescence-like features in the mouse pituitary gland. Mol. Cell Biol. 25, 2660–2672 (2005).

    CAS  Article  Google Scholar 

  16. 16

    Collado, M. & Serrano, M. Senescence in tumours: evidence from mice and humans. Nat. Rev. Cancer 10, 51–57 (2010).

    CAS  Article  Google Scholar 

  17. 17

    Di Leonardo, A., Linke, S. P., Clarkin, K. & Wahl, G. M. DNA damage triggers a prolonged p53-dependent G1 arrest and long-term induction of Cip1 in normal human fibroblasts. Genes Dev. 8, 2540–2551 (1994).

    CAS  Article  Google Scholar 

  18. 18

    Di Micco, R. et al. Oncogene-induced senescence is a DNA damage response triggered by DNA hyper-replication. Nature 444, 638–642 (2006).

    CAS  Article  Google Scholar 

  19. 19

    d'Adda di Fagagna, F. Living on a break: cellular senescence as a DNA-damage response. Nat. Rev. Cancer 8, 512–522 (2008).

    CAS  Article  Google Scholar 

  20. 20

    Narita, M. et al. Rb-Mediated heterochromatin formation and silencing of E2F target genes during cellular senescence. Cell 113, 703–716 (2003).

    CAS  Article  Google Scholar 

  21. 21

    Hemann, M. T. & Narita, M. Oncogenes and senescence: breaking down in the fast lane. Genes Dev. 21, 1–5 (2007).

    CAS  Article  Google Scholar 

  22. 22

    Di Micco, R., Fumagalli, M. & d'Adda di Fagagna, F. Breaking news: high-speed race ends in arrest - how oncogenes induce senescence. Trends Cell Biol. 17, 529–536 (2007).

    CAS  Article  Google Scholar 

  23. 23

    Zhang, R. et al. Formation of macroH2A-containing senescence-associated heterochromatin foci and senescence driven by ASF1a and HIRA. Dev. Cell 8, 19–30 (2005).

    CAS  Article  Google Scholar 

  24. 24

    Ye, X. et al. Definition of pRB- and p53-dependent and -independent steps in HIRA/ASF1a-mediated formation of senescence-associated heterochromatin foci. Mol. Cell Biol. 27, 2452–2465 (2007).

    CAS  Article  Google Scholar 

  25. 25

    Narita, M. et al. A novel role for high-mobility group A proteins in cellular senescence and heterochromatin formation. Cell 126, 503–514 (2006).

    CAS  Article  Google Scholar 

  26. 26

    Zhang, R., Chen, W. & Adams, P. D. Molecular dissection of formation of senescence-associated heterochromatin foci. Mol. Cell. Biol. 27, 2343–2358 (2007).

    CAS  Article  Google Scholar 

  27. 27

    Funayama, R. & Ishikawa, F. Cellular senescence and chromatin structure. Chromosoma 116, 431–440 (2007).

    Article  Google Scholar 

  28. 28

    Beausejour, C. M. et al. Reversal of human cellular senescence: roles of the p53 and p16 pathways. EMBO J. 22, 4212–4222 (2003).

    CAS  Article  Google Scholar 

  29. 29

    Itahana, K. et al. Control of the replicative life span of human fibroblasts by p16 and the polycomb protein Bmi-1. Mol. Cell Biol. 23, 389–401 (2003).

    CAS  Article  Google Scholar 

  30. 30

    Cortez, D., Guntuku, S., Qin, J. & Elledge, S. J. ATR and ATRIP: partners in checkpoint signaling. Science 294, 1713–1716 (2001).

    CAS  Article  Google Scholar 

  31. 31

    Mallette, F. A., Gaumont-Leclerc, M. F. & Ferbeyre, G. The DNA damage signaling pathway is a critical mediator of oncogene-induced senescence. Genes Dev. 21, 43–48 (2007).

    CAS  Article  Google Scholar 

  32. 32

    Hahn, W. C. et al. Creation of human tumour cells with defined genetic elements. Nature 400, 464–468 (1999).

    CAS  Article  Google Scholar 

  33. 33

    Rhodes, D. R. et al. ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia 6, 1–6 (2004).

    CAS  Article  Google Scholar 

  34. 34

    Kim, J-A., Kruhlak, M., Dotiwala, F., Nussenzweig, A. & Haber, J. E. Heterochromatin is refractory to γH2AX modification in yeast and mammals. J. Cell Biol. 178, 209–218 (2007).

    CAS  Article  Google Scholar 

  35. 35

    Murga, M. et al. Global chromatin compaction limits the strength of the DNA damage response. J. Cell Biol. 178, 1101–1108 (2007).

    CAS  Article  Google Scholar 

  36. 36

    Goodarzi, A. A. et al. ATM signaling facilitates repair of DNA double-strand breaks associated with heterochromatin. Mol. Cell 31, 167–177 (2008).

    CAS  Article  Google Scholar 

  37. 37

    Ziv, Y. et al. Chromatin relaxation in response to DNA double-strand breaks is modulated by a novel ATM- and KAP-1 dependent pathway. Nat. Cell Biol. 8, 870–876 (2006).

    CAS  Article  Google Scholar 

  38. 38

    Noon, A. T. et al. 53BP1-dependent robust localized KAP-1 phosphorylation is essential for heterochromatic DNA double-strand break repair. Nat. Cell Biol. 12, 177–184 (2010).

    CAS  Article  Google Scholar 

  39. 39

    Goodarzi, A. A., Jeggo, P. & Lobrich, M. The influence of heterochromatin on DNA double strand break repair: getting the strong, silent type to relax. DNA Repair (Amst) 9, 1273–1282 (2010).

    CAS  Article  Google Scholar 

  40. 40

    Rea, S. et al. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406, 593–599 (2000).

    CAS  Article  Google Scholar 

  41. 41

    Greiner, D., Bonaldi, T., Eskeland, R., Roemer, E. & Imhof, A. Identification of a specific inhibitor of the histone methyltransferase SU(VAR)3–9. Nat. Chem. Biol. 1, 143–145 (2005).

    CAS  Article  Google Scholar 

  42. 42

    Lachner, M., O'Carroll, D., Rea, S., Mechtler, K. & Jenuwein, T. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410, 116–120 (2001).

    CAS  Article  Google Scholar 

  43. 43

    Minucci, S. & Pelicci, P. G. Histone deacetylase inhibitors and the promise of epigenetic (and more) treatments for cancer. Nat. Rev. Cancer 6, 38–51 (2006).

    CAS  Article  Google Scholar 

  44. 44

    Altucci, L. & Minucci, S. Epigenetic therapies in haematological malignancies: searching for true targets. Eur. J. Cancer 45, 1137–1145 (2009).

    CAS  Article  Google Scholar 

  45. 45

    Bandyopadhyay, D. et al. Dynamic assembly of chromatin complexes during cellular senescence: implications for the growth arrest of human melanocytic nevi. Aging Cell 6, 577–591 (2007).

    CAS  Article  Google Scholar 

  46. 46

    George, P. et al. Combination of the histone deacetylase inhibitor LBH589 and the hsp90 inhibitor 17-AAG is highly active against human CML-BC cells and AML cells with activating mutation of FLT-3. Blood 105, 1768 –1776 (2005).

    CAS  Article  Google Scholar 

  47. 47

    Kim, I. A., Kim, I. H., Kim, H. J., Chie, E. K. & Kim, J. S. HDAC inhibitor-mediated radiosensitization in human carcinoma cells: a general phenomenon? J. Radiat. Res. (Tokyo) 51, 257–263 (2010).

    CAS  Article  Google Scholar 

  48. 48

    Herbig, U., Ferreira, M., Condel, L., Carey, D. & Sedivy, J. M. Cellular senescence in aging primates. Science 311, 1257 (2006).

    CAS  Article  Google Scholar 

  49. 49

    Scaffidi, P. & Misteli, T. Lamin A-dependent nuclear defects in human aging. Science 312, 1059–1063 (2006).

    CAS  Article  Google Scholar 

  50. 50

    Auth, T., Kunkel, E. & Grummt, F. Interaction between HP1α and replication proteins in mammalian cells. Exp. Cell Res. 312, 3349–3359 (2006).

    CAS  Article  Google Scholar 

  51. 51

    Humbert, N. et al. A genetic screen identifies topoisomerase 1 as a regulator of senescence. Cancer Res. 69, 4101–4106 (2009).

    CAS  Article  Google Scholar 

  52. 52

    Shimada, K. et al. Ino80 chromatin remodeling complex promotes recovery of stalled replication forks. Curr. Biol. 18, 566–575 (2008).

    CAS  Article  Google Scholar 

  53. 53

    Adams, P. D. Remodeling chromatin for senescence. Aging Cell 6, 425–427 (2007).

    CAS  Article  Google Scholar 

  54. 54

    Toledo, L. I., Murga, M., Gutierrez-Martinez, P., Soria, R. & Fernandez-Capetillo, O. ATR signaling can drive cells into senescence in the absence of DNA breaks. Genes Dev. 22, 297–302 (2008).

    CAS  Article  Google Scholar 

  55. 55

    Liontos, M. et al. Modulation of the E2F1-driven cancer cell fate by the DNA damage response machinery and potential novel E2F1 targets in osteosarcomas. Am. J. Pathol. 175, 376–391 (2009).

    CAS  Article  Google Scholar 

  56. 56

    Kang, M. Y. et al. Association of the SUV39H1 histone methyltransferase with the DNA methyltransferase 1 at mRNA expression level in primary colorectal cancer. Int. J. Cancer 121, 2192–2197 (2007).

    CAS  Article  Google Scholar 

  57. 57

    De Koning, L. et al. Heterochromatin protein 1α: a hallmark of cell proliferation relevant to clinical oncology. EMBO Mol. Med. 1, 13 (2009).

    Article  Google Scholar 

  58. 58

    Fanti, L., Giovinazzo, G., Berloco, M. & Pimpinelli, S. The heterochromatin protein 1 prevents telomere fusions in Drosophila. Mol. Cell 2, 527–538 (1998).

    CAS  Article  Google Scholar 

  59. 59

    Ayoub, N., Jeyasekharan, A. D. & Venkitaraman, A. R. Mobilization and recruitment of HP1: a bimodal response to DNA breakage. Cell Cycle 8, 2945–2950 (2009).

    PubMed  Google Scholar 

  60. 60

    Kim, J. A. & Haber, J. E. Chromatin assembly factors Asf1 and CAF-1 have overlapping roles in deactivating the DNA damage checkpoint when DNA repair is complete. Proc. Natl Acad. Sci. USA 106, 1151–1156 (2009).

    CAS  Article  Google Scholar 

  61. 61

    Moffat, J. & Sabatini, D. M. Building mammalian signalling pathways with RNAi screens. Nat. Rev. Mol. Cell Biol. 7, 177–187 (2006).

    CAS  Article  Google Scholar 

  62. 62

    Liontos, M. et al. Deregulated overexpression of hCdt1 and hCdc6 promotes malignant behavior. Cancer Res. 67, 10899–10909 (2007).

    CAS  Article  Google Scholar 

  63. 63

    Gargiulo, G. et al. NA-Seq: a discovery tool for the analysis of chromatin structure and dynamics during differentiation. Dev. Cell 16, 466–481 (2009).

    CAS  Article  Google Scholar 

  64. 64

    Ronzoni, S., Faretta, M., Ballarini, M., Pelicci, P. & Minucci, S. New method to detect histone acetylation levels by flow cytometry. Cytometry A 66, 52–61 (2005).

    Article  Google Scholar 

Download references

Acknowledgements

We thank M. Fumagalli for providing fibroblasts undergoing senescence following telomere shortening and for editing the manuscript; A. Oldani and D. Parazzoli from IFOM Imaging Unit for help with imaging; qRT–PCR and Cell Biology Units for support; S. Vultaggio for help with tumour xenograft generation and M. Romanenghi for technical assistance with ChIP. We thank O. Fernandez-Capetillo for pLKO.1 shATR; G. Smith for KU55933 (KuDOS Pharmaceuticals Ltd.). G. Manfioletti for sharing HMGA antibodies; P.P. Di Fiore for support; U. Herbig, B. Amati and M. Foiani for critical reading of the manuscript and all F.d'A.d.F. lab members for discussion and feedback throughout this work. M.L. and V.G. are funded by the European Commission (FP7-GENICA project). W.C.H. is supported in part by an U.S. NIH/NIA grant (ROI AG023145). The S.M. laboratory is supported in part by the European Union (Epitron). The F.d'A.d.F laboratory is supported by AIRC (Associazione Italiana per la Ricerca sul Cancro), the European Community's 7th Framework Programme (FP7/2007-2013) under grant agreement number 202230 (Genomic instability and genomic alterations in pre-cancerous lesions and/or cancer; GENINCA), HFSP (Human Frontier Science Program), AICR (Association for International Cancer Research), EMBO Young Investigator Program and Telethon.

Author information

Affiliations

Authors

Contributions

M.D. performed immunofluorescence microscopy experiments in Figs 2a and 7a and Supplementary Fig. S2a, and provided technical assistance for cell culture experiments. V.M. performed immunofluorescence microscopy experiments in Figs 2b and 6b and provided technical assistance for cell culture experiments. M.L. and V.G. generated and analysed data and images in Fig. 5a–g and Supplementary Fig. S3. O.A.B. generated data in Fig. 8b, c and Supplementary Fig. S7f, g. G.G. generated data in Fig. 4b and Supplementary Fig. S2l. R.d.Z. and C.M. generated and analysed data in Fig. 8d, e, f and Supplementary Fig. S8a. E.M. contributed to imaging analysis. G.d'A. performed statistical analysis on an imaging dataset. W.C.H. provided shRNA vectors and Ras transformed fibroblasts (ELR) and edited the manuscript. S.M. supervised O.A.B., R.d.Z. and C.M. work, contributed to experimental plan and edited the manuscript. R.D.M. and G.S. generated data of all remaining figures, assembled the manuscript and contributed to experimental design and manuscript writing. F.d'A.d.F. planned and supervised the project and wrote the manuscript.

Corresponding author

Correspondence to Fabrizio d'Adda di Fagagna.

Ethics declarations

Competing interests

S.M. has stocks in Genextra Spa, a biopharmaceutical company that is currently developing HDAC inhibitors for cancer therapy.

Supplementary information

Supplementary Information

Supplementary Information (PDF 2472 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Di Micco, R., Sulli, G., Dobreva, M. et al. Interplay between oncogene-induced DNA damage response and heterochromatin in senescence and cancer. Nat Cell Biol 13, 292–302 (2011). https://doi.org/10.1038/ncb2170

Download citation

Further reading

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing