Based on Glis1/Sox2 expression in 2D, we propose that NP stromal cells have a higher degree of stemness than FAT stromal cells, but a 3D environment and exposure to lactic acid appear to facilitate stemness in FAT cells and might elevate the risk of tumorigenesis for FAT stromal cells in the degenerate NP niche as indicated by higher Tbox (Tbx1) levels, a prognostic chordoma marker. This evidence concerns the gene SOX2 and chordoma.