Fig. 6

Genomic sequencing of CCA cell lines (A) Comparison of mutations identified in CCA cells and their original samples. Genes harboring mutations were classified into 5 categories: genome instability, epigenetic modifiers, DNA damage and cell cycle control, kinase RAS/RAF, and WNT signaling. Frequencies of mutations identified as tissue-specific, CCA cell-specific, or both cell- and tissue-specific. (B) Coding variants with preclinical or clinical evidence of treatment according to the OncoKb database (May 23rd, 2024). Each column represents a cell line. Green: Level 1; Pink: Level 3; Light Blue: Level 4; Orange: Likely pathogenic. The symbols are as follows: circle, truncating mutation; triangle, missense mutation. (C) Annotated alterations in TP53 and KRAS were detected in CCA cell lines. (D) A representative image of the sequencing traces of amplified TP53 (NM_000546) and KRAS (NM_004985) in the KKU-100, KKU-466, KKU-610, and KKU-097 cell lines is shown. The red triangle and square represent point mutation and nucleotide insertion, respectively. (E) Principal component analysis (PCA) score plot of the mutational spectrum data showing the separation between the older set (yellow dots) and the new set (purple dots) of established CCA cell lines. (F) PCA loading plot highlighting the gene set contributing to the PC1 loading variable. The blue bars indicate the gene set contributing to the negative loading, which correlates with the older group of CCA cell lines; the red bars indicate the gene set contributing to the positive loading, which is associated with the newly established group of CCA cell lines.