Identifying potential biomarkers for colorectal cancer diagnosis using an RNA-seq analysis workflow
In South Africa, colorectal cancer (CRC) is the second most common cancer in men and the third most common cancer in women, located at the lower end of the digestive system, in the colon and rectum, and is most accurately diagnosed through colonoscopy procedures. The prevalence of CRC is on the rise globally as well as locally, yet participation rates for screening tools remain low. In the present study, bioinformatics which is a multidisciplinary field that is focused on interpreting biology through the analysis of gene sequences and protein expression, was employed to explore the molecular biology of patient CRC data as well as to identify dysregulated genes as potential biomarkers to be used as an alternative screening tool. This was performed by creating an RNA-Seq analysis workflow, that identified differentially expressed genes that were further used in functional analysis to identify biological processes and pathways relating to CRC onset and progression in patients. The genes were tested as biomarkers in silico using statistical tests and blood expression data and the genes identified included COL11A1, INHential tissue biomarkers, and MMP1, CTHRC1, KRT17 and IGBA, CLDN1, ETV4 and FOXQ1 as potFBP1 as potential blood biomarkers. The identified biomarkers require future wet lab validation and illustrates the potential for a novel CRC screening test to reduce the dependency on traditional tools that are ineffective due to poor patient participation and associated cost.
A dissertation submitted in fulfilment of the requirements for the degree of Master of Science to the Faculty of Science, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, 2021