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Genome-wide DNA methylation profiling reveals cancer-associated changes within early colonic neoplasia

Oncogene volume 36, pages 5035–5044 (2017)Cite this article

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Abstract

Colorectal cancer (CRC) is characterized by genome-wide alterations to DNA methylation that influence gene expression and genomic stability. Less is known about the extent to which methylation is disrupted in the earliest stages of CRC development. In this study, we have combined laser-capture microdissection with reduced representation bisulfite sequencing to identify cancer-associated DNA methylation changes in human aberrant crypt foci (ACF), the earliest putative precursor to CRC. Using this approach, methylation profiles have been generated for 10 KRAS-mutant ACF and 10 CRCs harboring a KRAS mutation, as well as matched samples of normal mucosa. Of 811 differentially methylated regions (DMRs) identified in ACF, 537 (66%) were hypermethylated and 274 (34%) were hypomethylated. DMRs located within intergenic regions were heavily enriched for AP-1 transcription factor binding sites and were frequently hypomethylated. Furthermore, gene ontology analysis demonstrated that DMRs associated with promoters were enriched for genes involved in intestinal development, including homeobox genes and targets of the Polycomb repressive complex 2. Consistent with their role in the earliest stages of colonic neoplasia, 75% of the loci harboring methylation changes in ACF were also altered in CRC samples, though the magnitude of change at these sites was lesser in ACF. Although aberrant promoter methylation was associated with altered gene expression in CRC, this was not the case in ACF, suggesting the insufficiency of methylation changes to modulate gene expression in early colonic neoplasia. Altogether, these data demonstrate that DNA methylation changes, including significant hypermethylation, occur more frequently in early colonic neoplasia than previously believed, and identify epigenomic features of ACF that may provide new targets for cancer chemoprevention or lead to the development of new biomarkers for CRC risk.

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Acknowledgements

This work was supported by NIH grant CA159976 to DWR, and NIH grants CA084469 and CA160965 to GPP.

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Author notes

  1. M P Hanley and M A Hahn: These authors contributed equally to this work.

Authors and Affiliations

  1. Center for Molecular Medicine, School of Medicine, UConn Health, Farmington, CT, USA

    M P Hanley & D W Rosenberg

  2. Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA

    M P Hanley & D W Rosenberg

  3. Department of Surgery, City of Hope, Duarte, CA, USA

    M A Hahn, A H Choi & Y Fong

  4. Department of Information Sciences, City of Hope, Duarte, CA, USA

    A X Li

  5. Department of Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA

    X Wu

  6. The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA

    J Lin & Z Ouyang

  7. Integrative Genomics Core, Beckman Research Institute, City of Hope, Duarte, CA, USA

    J Wang

  8. Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA

    Z Ouyang

  9. Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA

    G P Pfeifer

  10. Division of Gastroenterology, School of Medicine, UConn Health, Farmington, CT, USA

    T J Devers

  11. Colon Cancer Prevention Program, Neag Comprehensive Cancer Center, UConn Health, Farmington, CT, USA

    D W Rosenberg

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Hanley, M., Hahn, M., Li, A. et al. Genome-wide DNA methylation profiling reveals cancer-associated changes within early colonic neoplasia. Oncogene 36, 5035–5044 (2017). https://doi.org/10.1038/onc.2017.130

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