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  • Oncogenomics
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Chromatin H3K27me3/H3K4me3 histone marks define gene sets in high-grade serous ovarian cancer that distinguish malignant, tumour-sustaining and chemo-resistant ovarian tumour cells

Oncogene volume 32, pages 4586–4592 (2013)Cite this article

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Abstract

In embryonic stem (ES) cells, bivalent chromatin domains containing H3K4me3 and H3K27me3 marks silence developmental genes, while keeping them poised for activation following differentiation. We have identified gene sets associated with H3K27me3 and H3K4me3 marks at transcription start sites in a high-grade ovarian serous tumour and examined their association with epigenetic silencing and malignant progression. This revealed novel silenced bivalent marked genes, not described previously for ES cells, which are significantly enriched for the PI3K (P<10−7) and TGF-β signalling pathways (P<10−5). We matched histone marked gene sets to gene expression sets of eight normal fallopian tubes and 499 high-grade serous malignant ovarian samples. This revealed a significant decrease in gene expression for the H3K27me3 and bivalent gene sets in malignant tissue. We then correlated H3K27me3 and bivalent gene sets to gene expression data of ovarian tumour ‘stem cell-like’ sustaining cells versus non-sustaining cells. This showed a significantly lower expression for the H3K27me3 and bivalent gene sets in the tumour-sustaining cells. Similarly, comparison of matched chemo-sensitive and chemo-resistant ovarian cell lines showed a significantly lower expression of H3K27me3/bivalent marked genes in the chemo-resistant compared with the chemo-sensitive cell line. Our analysis supports the hypothesis that bivalent marks are associated with epigenetic silencing in ovarian cancer. However it also suggests that additional tumour specific bivalent marks, to those known in ES cells, are present in tumours and may potentially influence the subsequent development of drug resistance and tumour progression.

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Acknowledgements

This work was supported by funding from Ovarian Cancer Action; and Cancer Research UK; as well as the Imperial Experimental Cancer Research and Biomedical Research Centres. We are grateful for help from the Gynaecological Oncology team at Hammersmith Hospital and members of the Ovarian Cancer Action Research Centre, in particular Elham Shamsaei, Nona Rama, and Kay Dawson from Dept Pathology. We thank Prof Edison T Liu, Genome Institute of Singapore, and the Agency for Science Technology and Research of Singapore for supporting the microarray expression data on the ovarian tumour and benign samples. Gene expression data generated by The Cancer Genome Atlas (TCGA) Pilot Project established by the NCI and NHGRI were used in the study.

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  1. N Chapman-Rothe and E Curry: The authors wish it to be known that, in their opinion, the first 2 authors should be regarded as joint First Authors.

Authors and Affiliations

  1. Department of Surgery & Cancer, Epigenetic Unit, Imperial College London, Hammersmith Campus, London, UK

    N Chapman-Rothe, C Zeller, D Liber, S Ghaem-Maghami & R Brown

  2. Ovarian Cancer Action Research Centre, Imperial College London, Hammersmith Campus, London, UK

    E Curry, D Liber, E Stronach, H Gabra & R Brown

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  1. N Chapman-Rothe
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Correspondence to R Brown.

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Chapman-Rothe, N., Curry, E., Zeller, C. et al. Chromatin H3K27me3/H3K4me3 histone marks define gene sets in high-grade serous ovarian cancer that distinguish malignant, tumour-sustaining and chemo-resistant ovarian tumour cells. Oncogene 32, 4586–4592 (2013). https://doi.org/10.1038/onc.2012.477

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