DNA Methylation in Rectal Cancer

Abstract

Rectal cancer differs from colon cancer in terms of its underlying biological behaviour, clinical course, genetic and epigenetic aetiology. Epigenetic mechanisms modify gene expression independently of DNA sequence. DNA methylation is the most studied epigenetic mechanism, known to play a role in colorectal cancer. The role of DNA methylation specific to rectal cancer however, is poorly understood. Here we present the results from a DNA methylation study of 45 individuals with rectal cancer. A total of 45 patients (>18 years) diagnosed with rectal adenocarcinoma (stages II and III) who underwent or were undergoing treatment were recruited. Matched rectal tumour and adjacent normal mucosal samples (n=90) were obtained from each patient and processed fresh frozen (n=32) or embedded in paraffin (n=58). DNA was extracted and checked for quality and quantity, treated with sodium bisulfite and run on the Illumina Infinium HumanMethylation 450 Beadchip. Only samples that passed the Quality Control were subsequently analysed (n=30). A combined linear regression analysis of all 408,652 probes showed that global levels of DNA methylation are decreased in rectal cancer samples compared with normal unaffected samples. In total, 176 differentially methylated probes and 828 differentially methylated regions were identified in rectal cancer vs normal tissue. All the genes identified underwent gene ontology analysis to assess whether they are biologically meaningful. In summary, our study focused on the discovery of de novo epigenetic changes associated with rectal cancer, using a genome wide approach and novel bioinformatics approaches. These findings improve our understanding of the epigenetics of this disease. Furthermore, they have the potential to be used as biomarkers for detection, prognosis and monitoring treatment response in patients with rectal cancer.