Generation of patient specific iPSC-derived healthy organoids from primary colorectal cancer patients with/without metastasis and transcriptome analysis

Cancer is a multifactorial disease with high mortality and incidence rate. Colorectal cancer (CRC) is a type of gastrointestinal cancer and causes about 700,000 deaths worldwide every year. Although CRC propagation mechanisms are partially explained by genetic factors, a clear cancer initiation mechanism has not been revealed. Age and environmental factors are particularly prominent in non-hereditary (sporadic) CRC formation, but it is still unknown how and why certain colon cells are affected by such factors. Early diagnosis is vital for CRC, as in other types of cancer. The most reliable diagnostic method is the pathological examination of suspicious tissue biopsies taken during colonoscopy in the distal colon and rectum. However, since the perceptible symptoms of CRC patients are usually at more advanced stages, it is not practical to apply such an invasive method for early diagnosis to individuals who do not yet have any complaints. For this reason, it is very important to develop new methods for the early diagnosis of sporadic CRC development. Induced pluripotent stem cells (iPSCs) are formed by transferring certain pluripotent transcription factors (Oct4, Sox2, Klf4, c-Myc) into somatic cells. The most basic feature of iPSCs, which are reprogrammed to the embryonic stem cell stage, is their ability to differentiate into cell types of three germ layers. The fact that the cell models currently used in cancer studies simulate the final stages of cancer limits in vitro studies from being able to study cancer initiation and development. In particular, iPSCs show promise for early diagnosis and determination of appropriate treatment. In this thesis study, we reprogrammed erythroid progenitor cells from peripheral blood of CRC patients into iPSCs by using the Sendai viral system. After that, we differentiated iPSCs into colon organoids. Following the development of healthy colon organoids of CRC patients, transcriptome analysis was done by RNA sequencing. Whether there were transcriptomic patterns that may cause susceptibility to cancer formation in individuals who develop CRC. In this way, it was assessed to see if there were any trends at the transcriptome level in people who had CRC that would indicate a susceptibility to cancer. After this thesis was successfully completed, it was discovered that the pathways already linked to cancer were expressed differently in healthy colon organoids from CRC patients in comparison with the donors without a history of cancer. Also, it was shown that the expression of gene clusters linked to the epithelial-mesenchymal transition shifted between healthy colon organoids from patients with and without metastases.