The Role of Epigenetics in Hereditary Colorectal Cancer Tumorigenesis: Validation of Genome-Wide Methylation Array Results through Bisulfite Sequencing

Colorectal cancer (CRC) poses a considerable global health challenge, with high mortality rates despite advancements in cancer research. Approximately one in ten CRC cases have a hereditary basis, with Lynch syndrome and Familial adenomatous polyposis standing as the two predominant cancer-predisposing syndromes. These conditions are mainly attributed to specific dominant germline mutations in CRC-related genes. However, as the role of epigenetic modifications, including DNA methylation, has become increasingly recognized in colorectal tumorigenesis, identifying these distinct signatures is paramount in gaining deeper insights into the molecular mechanisms underlying CRC. This thesis, conducted as a part of ongoing research into the DNA methylation profile of Lynch syndrome and Familial adenomatous polyposis-associated colorectal tumors, aimed to validate methylation patterns previously obtained from a genome-wide Illumina Methylation EPIC BeadChip array. The validation was performed by utilizing direct bisulfite sequencing across 12 selected gene regions on CRC cell lines and histologically normal control samples and comparing the methylation status to the EPIC array results. The genomic regions selected for this analysis were chosen based on differential methylation observed with EPIC and literature and were limited to regions that included at least one GCGC site for the HhaI digestion enzyme for future in-house MS-MLPA probe design. The results of this study demonstrate a clear differential methylation pattern of the selected genes, with CRC cell lines generally exhibiting higher methylation levels compared to non-cancerous samples, as expected. Specifically, high concordance between EPIC results and bisulfite sequencing data was observed in the methylation status of ADHFE1, EYA4, ITGA4, FBLIM1, and SEPT9, whose connection to CRC has been also shown in the previous studies. Further investigations of the genes in this study could contribute to a better understanding of epigenetic changes underlying colorectal tumors and hold the potential for developing novel biomarkers for early diagnosis and improved patient prognosis.

Grantor dc:publisher

Helsingin yliopisto

Year dc:date.issued

2024

Author dc:creator

• Puustinen, Taru

Contributors dc:contributor

• Helsingin yliopisto, Bio- ja ympäristötieteellinen tiedekunta
• University of Helsinki, Faculty of Biological and Environmental Sciences
• Helsingfors universitet, Bio- och miljövetenskapliga fakulteten

• adenoma
• bisulfite sequencing
• Colorectal cancer
• CIMP
• DNA methylation
• Familial adenomatous polyposis
• hereditary CRC
• Lynch syndrome
• microsatellite instability

Language dc:language.iso

eng

Identifier URI

URN:NBN:fi:hulib-202406112671

OAI identifier oai:identifier

oai:helda.helsinki.fi:10138/576810