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Oncogene-induced replication stress preferentially targets common fragile sites in preneoplastic lesions. A genome-wide study

Oncogene volume 27, pages 3256–3264 (2008)Cite this article

Abstract

Common fragile sites (CFSs) are regions of the genome prone to breakage by replication inhibitors (extrinsic replication stress). Recently, we and others observed that oncogene-induced replication stress (RS) induces DNA damage from the earliest stages of cancer. Our aim was to perform a genome-wide analysis in precancerous and cancerous experimental models to examine whether allelic imbalance occurs within CFSs. Subsequently, CFSs sequence characteristics were assessed. We used a growth-factor-induced human skin hyperplasia and a H-ras-induced mouse hyperplastic urothelium as preneoplastic models, along with an inducible U2OS-CDT1Tet-ON cancer cell line model, all bearing established oncogene-induced RS stimuli. Human DNA was analysed with Affymetrix SNP microarrays, while mouse DNA was analysed with Nimblegen array CGH. We studied 56 aphidicolin-type CFSs and 1914 regions of control, nonfragile DNA. Our theoretical in silico analysis spanned 2.16 billion nonoverlapping bases on human chromosomes 1–22. Our results provide direct experimental evidence indicating that genomic alterations were more common within CFSs in epidermal and urothelial preneoplastic lesions as well as in cancer. CFSs were on average less flexible than nonfragile regions, contained more guanine–cytosine (GC) and Alu sequences. Importantly, regions with loss-of-heterozygosity were also less flexible and had a higher Alu percentage.

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Abbreviations

AI:

allelic imbalance

CFSs:

common fragile sites

CGH:

comparative genomic hybridization

FS:

fragile sites

GF-hSHy:

growth-factor-induced human skin hyperplasia

H-ras-mHyU:

H-ras-induced mouse hyperplastic urothelium

RS:

replication stress

SNP:

single nucleotide polymorphism

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Acknowledgements

We thank Professor Meenhard Herlyn for providing the human skin xenograft material. This work was co-funded by European Social Fund and National Resources-(EPEAEK-II) PYTHAGORAS II (SARG 7952) and National Kapodistrian University of Athens (SARG 56/90/6599, 70/4/9174).

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Authors and Affiliations

  1. Department of Histology and Embryology, Molecular Carcinogenesis Group, School of Medicine, University of Athens, Athens, Greece

    P K Tsantoulis, A Kotsinas, K Evangelou, M Sideridou, C Kittas & V G Gorgoulis

  2. First Department of Propedeutic and Internal Medicine, School of Medicine, University of Athens, Athens, Greece

    P P Sfikakis

  3. Clinical Cytogenetics Laboratory, College of Physicians and Surgeons of Columbia University, New York, USA

    B Levy

  4. Department of Urology, New York University School of Medicine, New York, USA

    L Mo & X-R Wu

  5. Department of Biochemistry, School of Medicine, University of Athens, Athens, Greece

    A G Papavassiliou

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  1. P K Tsantoulis
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  2. A Kotsinas
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  4. K Evangelou
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Correspondence to A G Papavassiliou or V G Gorgoulis.

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Supplementary Information accompanies the paper on the Oncogene website (http://www.nature.com/onc).

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Tsantoulis, P., Kotsinas, A., Sfikakis, P. et al. Oncogene-induced replication stress preferentially targets common fragile sites in preneoplastic lesions. A genome-wide study. Oncogene 27, 3256–3264 (2008). https://doi.org/10.1038/sj.onc.1210989

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