Epigenome-Wide Analysis of DNA Methylation Reveals a Rectal Cancer-Specific Epigenomic Signature

Abstract

Aim: The aim of the present study is to address a genome-wide search for novel methylation biomarkers in the rectal cancer (RC), as only scarce information on methylation profile is available. Materials & methods: We analyzed methylation status in 25 pairs of RC and adjacent healthy mucosa using the Illumina Human Methylation 450 BeadChip. Results: We found significantly aberrant methylation in 33 genes. After validation of our results by pyrosequencing, we found a good agreement with our findings. The BPIL3 and HBBP1 genes resulted hypomethylated in RC, whereas TIFPI2, ADHFE1, FLI1 and TLX1 were hypermethylated. An external validation by TCGA datasets confirmed the results. Conclusion: Our study, with external validation, has demonstrated the feasibility of using specific methylated DNA signatures for developing biomarkers in RC.

Keywords::

• DNA methylation
• Illumina Human Methylation 450 BeadChip
• rectal cancer

Supplementary data

To view the supplementary data that accompany this paper please visit the journal website at: www.tandfonline.com/doi/full/10.2217/epi-2016-0044

Acknowledgements

The authors are very thankful to E Van Emburgh for his technical support.

Financial & competing interests disclosure

SEQ Technology Platform in Uppsala. The platform is part of Science for Life Laboratory at Uppsala University and supported as a national infrastructure by the Swedish Research Council. This work was supported by the Internal Grant Agency of the Czech Ministry of Health (NT 13424, NT/14329-3), Czech Science Foundation (15-27580A; GA15-08239S), COST LD14050 and by the European Regional Development Fund (project number CZ.1.05/2.1.00/03.0076), Lions Cancer Foundation and Nyckelfonden, Örebro läns landstin. This study was also supported by the National Sustainability Program I (NPU I) Nr. LO1503 provided by the Ministry of Education Youth and Sports of the Czech Republic. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Additional information

Funding

SEQ Technology Platform in Uppsala. The platform is part of Science for Life Laboratory at Uppsala University and supported as a national infrastructure by the Swedish Research Council. This work was supported by the Internal Grant Agency of the Czech Ministry of Health (NT 13424, NT/14329-3), Czech Science Foundation (15-27580A; GA15-08239S), COST LD14050 and by the European Regional Development Fund (project number CZ.1.05/2.1.00/03.0076), Lions Cancer Foundation and Nyckelfonden, Örebro läns landstin. This study was also supported by the National Sustainability Program I (NPU I) Nr. LO1503 provided by the Ministry of Education Youth and Sports of the Czech Republic. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.