Loss of CD90 alters EMT-associated features and drug sensitivity in U-CH1 chordoma cells

Chordoma is a rare, slow-growing malignancy of notochordal origin characterized by a high degree of chemoresistance and limited therapeutic responsiveness. Despite advances in molecular profiling, the mechanisms underlying its cellular plasticity and therapy evasion remain incompletely defined. Emerging evidence across solid tumors suggests that cancer stem-like cells (CSCs) and the epithelial-to-mesenchymal transition (EMT) play central roles in driving tumor progression, metastatic potential, and drug resistance. These phenotypes are frequently orchestrated by surface glycoproteins. Among them, CD90 (THY1)-a glycosylphosphatidylinositol-anchored membrane protein-has been shown to regulate stemness, EMT activation, and chemoresistance in various epithelial and mesenchymal tumors. However, the functional relevance of CD90 in the pathophysiology of chordoma remains unclear. To explore this, a CRISPR/Cas9-mediated CD90 knockout was performed in U-CH1 cells. Results show that CD90 knockout in chordoma induced morphological changes consistent with EMT, and upregulated EMT-related transcription factors, and increased migratory and invasive capacity. This was accompanied by a G1 phase delay, reduced proliferation, and elevated expression of pluripotency markers. CD90-deficient cells displayed diminished sphere formation and downregulation of self-renewal-associated genes (CD24, ABCG2). Given the concurrent suppression of inflammation-related mediators (IL6, LIF, TNF)-previously implicated in chordoma chemoresistance-drug sensitivity profiling was performed, revealing increased responsiveness to metformin and etoposide, while sensitivity to methotrexate remained unchanged. Collectively, these findings identify CD90 as a multifaceted regulator of chordoma cell behavior-modulating self-renewal, drug response, and EMT-highlighting the need for therapeutic strategies informed by the complex interplay of these pathways.