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Lineage-specific RUNX3 hypomethylation marks the preneoplastic immune component of gastric cancer

Oncogene volume 34, pages 2856–2866 (2015)Cite this article

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Abstract

Runt domain transcription factor 3 (RUNX 3) is widely regarded as a tumour-suppressor gene inactivated by DNA hypermethylation of its canonical CpG (cytidine-phosphate-guanidine) island (CGI) promoter in gastric cancer (GC). Absence of RUNX3 expression from normal gastric epithelial cells (GECs), the progenitors to GC, coupled with frequent RUNX3 overexpression in GC progression, challenge this longstanding paradigm. However, epigenetic models to better describe RUNX3 deregulation in GC have not emerged. Here, we identify lineage-specific DNA methylation at an alternate, non-CGI promoter (P1) as a new mechanism of RUNX3 epigenetic control. In normal GECs, P1 was hypermethylated and repressed, whereas in immune lineages P1 was hypomethylated and widely expressed. In human GC development, we detected aberrant P1 hypomethylation signatures associated with the early inflammatory, preneoplastic and tumour stages. Aberrant P1 hypomethylation was fully recapitulated in mouse models of gastric inflammation and tumorigenesis. Cell sorting showed that P1 hypomethylation reflects altered cell-type composition of the gastric epithelium/tumour microenvironment caused by immune cell recruitment, not methylation loss. Finally, via long-term culture of gastric tumour epithelium, we revealed that de novo methylation of the RUNX3 canonical CGI promoter is a bystander effect of oncogenic immortalization and not likely causal in GC pathogenesis as previously argued. We propose a new model of RUNX3 epigenetic control in cancer, based on immune-specific, non-CGI promoter hypomethylation. This novel epigenetic signature may have utility in early detection of GC and possibly other epithelial cancers with premalignant immune involvement.

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Acknowledgements

We thank Professor Y Groner and Dr D Levanon (The Weizmann Institute of Science, Rehovot, Israel) for their gift of anti-Runx3 antiserum and critical reviews of the manuscript. We thank Professor I van Driel (University of Melbourne, Australia) for providing H+/K+ ATPase-gmcsf transgenic mice and Professor M Ernst (Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia) for providing gp130F/F mice. We thank Dr J Däbritz (Murdoch Children’s Research Institute) for critically reviewing the manuscript. This work was supported by a project grant (1006542) awarded to TRM by the National Health and Medical Research Council (NH&MRC) of Australia and by the Victorian Government’s Medical Research Operational Infrastructure Program.

Author Contributions

TRM, ASG, LMJ and JRM conceived, designed and led the study. BK, TRM, EK and RHW performed the experiments. BK and TRM analysed the data. TM and JGF contributed reagents and materials. TRM and BK wrote the manuscript. TRM, ASG, LMJ and JRM edited and revised the manuscript. All authors approved the final version of the manuscript before submission

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  1. A S Giraud and T R Menheniott: These authors contributed equally to this work.

Authors and Affiliations

  1. Infection and Immunity, Murdoch Children’s Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia,

    B Kurklu, E K Ong, J R Mann, L M Judd, A S Giraud & T R Menheniott

  2. Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia

    B Kurklu, R H Whitehead, L M Judd, A S Giraud & T R Menheniott

  3. Division of Translational and Clinical Oncology, Cancer Research Institute, Kanazawa University, Kanazawa, Japan

    T Minamoto

  4. Division of Comparative Medicine, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA

    J G Fox

  5. Department of Zoology, University of Melbourne, Melbourne, Victoria, Australia

    J R Mann

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Kurklu, B., Whitehead, R., Ong, E. et al. Lineage-specific RUNX3 hypomethylation marks the preneoplastic immune component of gastric cancer. Oncogene 34, 2856–2866 (2015). https://doi.org/10.1038/onc.2014.233

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