Identification of genomic and transcriptomic variants in chordoma cancer stem cells

Chordoma is a rare malignant bone tumor that originates from remnants of the embryonic notochord. Since a reliable treatment for chordoma has not yet been developed, determining the factors that contribute to the pathogenesis of chordoma is of great importance in terms of understanding the disease to develop new targets for treatment. In this dissertation study, prominent genomic variations and molecular pathways in chordoma cancer stem cells were investigated. For this purpose, initially, chordoma tumorspheres, side populations, and CD133+ and CD15+ double-positive cells were enriched in 4 different chordoma cell lines, and the obtained cells were compared in terms of expression changes in stemness and EMT marker genes. Among the techniques that were examined, the tumorsphere enrichment method was determined to be applicable for four chordoma cell lines. Then, genomic variations and differential gene expression profiles of chordoma tumorspheres were determined by next-generation DNA sequencing and total transcriptome microarray techniques. Functional enrichment analyses were used for the evaluation and determination of dysregulated pathways in chordoma tumorspheres in comparison to parental cell lines. Finally, gene expression of SEMA5A, TPD52L1, and GAPLINC genes, whose expression was found to be upregulated in tumorspheres, were inhibited in two chordoma cell lines to investigate their downstream effects on invasion, migration, and viability. Results showed that siRNA-mediated silencing of TPD52L1 significantly impairs both the migration and invasion characteristics of chordoma cell lines. Downregulation of SEMA5A inhibited migration and invasion of UM-Chor1 cells and impaired the invasive capacity of MUG-Chor1 cells. Additionally, decreased GAPLINC expression significantly reduced invasion and migration in UM-Chor1 cells, but did not affect MUG-Chor1 cells. This study constitutes a first in the literature in terms of examining genomic and transcriptomic changes in tumorsphere-derived chordoma cancer stem cells as well as demonstrating the impact of TPD52L1 and SEMA5A genes on the invasive and migrative capacity of chordoma cells.