Functional and Genetic TP53 Status in Cell Lines

The functional and genetic TP53 status of 966 cell lines was determined using the Cancer Cell Line Encyclopedia (CCLE; see URLs)⁴⁴ , Genomics of Drug Sensitivity in Cancer (GDSC; see URLs)⁴⁵ , Cancer Target Discovery and Development (CTD²; see URLs)⁴⁶ , and The Cancer Genome Atlas (TCGA accessed via cBioPortal; see URLs)⁴⁷ databases. Cell lines were first separated into two functional classes by considering nutlin-3 sensitivity data from GDSC and CTD², and a p53 target gene expression signature⁴⁸ computed using CCLE data. Each cell line was provisionally considered as p53 functional if the functional score (calculated as [Target Genes CCLE Z-score] - [Nutlin-3 CTD² Z-score] - [Nutlin-3 Sanger Z-score]) was above 0, and provisionally considered as p53 non-functional if this value was below 0. Cell lines in the p53 functional class were declared p53 wild-type (WT) if no TP53 alterations were detected by CCLE, GDSC, or TCGA (n = 252), and discarded as ambiguous if any TP53 alterations were found (n = 104). Cell lines in the p53 non-functional class were declared p53 mutant if any genetic TP53 alteration was found (n = 528) and discarded as ambiguous if no TP53 alterations were found (n = 82). The p53 mutant class was further divided into four subclasses: a loss-of-function (LOF) subclass, comprising cell lines with nonsense mutations, frameshift mutations, or homozygous deletions; a missense subclass; a splice-site subclass; and an in-frame insertion/deletion subclass. Cell lines with multiple TP53 alterations were classified using the following precedence order: missense > in-frame > splice site > LOF. Refer to Supplementary Table 1 for the full classification matrix.