Identification of aberrant epigenetic events in MSS/CIMP-negative colon cancer

Ph.D. University of Hawaii at Manoa 2014.Includes bibliographical references.My research project focused on the identification of aberrant epigenetic changes via non-coding RNAs and DNA methylation in MSS/CIMP-negative colon cancer, the major subtype. DNA methylation is the most well studied epigenetic event, while non-coding RNA-mediated transcriptional silencing has also an important role in cancer. My first aim was to profile microRNAs and their potential target genes in colon cancer by a study of 10 paired normal and tumor colon tissues using data from Next Generation Sequencing and Exon arrays. Nineteen miRNAs, including 6 previously colon cancer associated and 13 not previously implicated, were found aberrantly expressed in the tumor tissues. Thirty-six colon cancer related genes were significantly correlated to the expression levels of the identified miRNAs and 'Wnt/beta-catenin Signaling' was identified as the top canonical pathway for these target genes. My second aim was to identify small and long novel non-coding RNAs at the 8q24 region which contains one of the most relevant colon cancer risk variants, SNP rs6983267. Thirty-two pre-miRNAs were identified In Silico by two algorithms, but none of them were verified in further studies. However, a novel long non-coding RNA spanning the rs6983267 was recently identified, and significantly elevated expression levels were observed in 23 colon tumor tissues in our sample set. Also, one known miRNA in a cluster 400 kb away from the risk SNP showed genotype dependent expression patterns. My last aim was to elucidate the landscape of genome-wide DNA methylation in colon cancer. General hypomethylation was observed, concentrating in the intergenic regions and gene bodies, while hypermethylation was observed in promoter regions, N_Shores and CpG islands. Differentially methylated CpGs were enriched in genes with roles in cancer and gastrointestinal disease. Observations in imprinted genes suggest a more widespread dysregulation of imprinting in colon cancer than previously reported. The findings of epigenetic alterations in colon cancer will hopefully contribute to a better understanding of these aberrant events: how they are related to colon cancer development and progression, while these findings may also lead to discovery of new biomarkers that can be utilized in patient diagnosis, stratification and the follow-up of the treatment