Cancer stem cell isolation from chordoma cell lines: Integrated miRNA-mRNA analysis of the cancer stem cells

Chordoma is a rare, slowly growing tumor which is thought to originate from remnants of embryonic notochord associated with an aggressive outcome. Cancer stem-like cells (CSCs) are thought to be related to tumorigenesis, recurrence, and resistance in cancers. CD133+CD15+ cells exhibited CSC phenotype with increased CSC- and Epithelial-Mesenchymal Transition (EMT)-related gene expression, invasion, migration, tumorosphere- and colony-forming abilities. In this study, differentially expressed miRNAs and mRNAs were determined in CSCs and their role in chordoma development was identified. WNT5A, TGF-α, BTG2 and MYCBP genes involved in CSC-related pathways, were targets of miR-140-3p, miR-148a-3p, miR-210-5p and miR-574-5p, respectively. Transfection of CSC-related miRNAs elevated migration and invasion capability along with stem cell phenotype. To show the concordance between in-vitro tests and patient data, fresh frozen chordoma tissues were used. The results showed that miR-140-3p and miR-148a-3p expressions were found to be associated with Ki67 while miR-140-3p and TGF-α expressions associated with p53 expression. Moreover, MYCBP expression that is positively associated with tumor volume and metastasis was correlated with the expression of miR-210-5p and TGF-α in our patient cohort. In addition, mRNA microarray analysis revealed that 226 mRNAs were dysregulated in recurrent chordoma samples in comparison to primary chordoma samples. High expression of both LGR5 and IGFBP2 was associated with poor prognosis in chordoma. In addition to these results, herein, a recurrent-clivus chordoma cell line firstly established and named as YU-Chor1. Based on the findings, chordoma CD133+CD15+ cells had unique miRNA profile, which can regulate stem-like properties of chordoma CSCs. This study was supported by TÜBİTAK as a 3501-Career Project (Grant number: 112S485) and Yeditepe University Hospital.