Fig. 2: Effect of TP53 loss in BE with CDKN2A LoF.
a, Frequency of CDKN2A LoF in 356 BEs (n = 257 P-BE and n = 99 NP-BE individuals, respectively) with or without TP53 LoF. Statistical significance was assessed using a two-sided Fisher’s exact test (P = 0.05). b, Frequency of EACs with clonal LoF alterations in CDKN2A and TP53 genes. For this analysis, n = 580/779 patients with EAC with WGS or WES data and LoF in these genes were considered. Statistical significance was assessed using a two-sided Fisher’s exact test (P = 0.001). c, Frequency of EACs with clonal and subclonal LoF alterations in CDKN2A and TP53 genes in n = 47 patients with WGS or WES data and damaging alterations in both genes. d, CDKN2A and TP53 gene expression levels quantified by RT–qPCR of RNA from TP53 wild-type CP-A cells (CP-A_TP53wt), three TP53 KO clones (CP-A_2c8, CP-A_3d2, CP-A_5f4) and control RNA relativized to ACTB expression. One biological replicate was performed with three technical replicates. e, TP53 gene structure in CP-A_TP53wt, CP-A_2c8, CP-A_3d2 and CP-A_5f4 cells. Exon-intron arrangement was derived from the UCSC genome browser (https://genome.ucsc.edu/) based on NM_000546 mRNA sequence (chr17:7,668,421-7,687,490, hg38 assembly). Dotted lines represent edited regions. f, Growth curves of CP-A_TP53wt, CP-A_2c8, CP-A_3d2 and CP-A_5f4 cells. Proliferation was assessed every 24 h and normalized to time zero. Mean values at 72 h were compared by two-tailed Student’s t-test (P = 1 × 10−4, 8 × 10−6 and 2 × 10−7, respectively). Error bars show standard deviation. Three biological replicates were performed, each in two to four technical replicates. ctrl, control; KO, knockout; P-BE, progressor Barrett’s esophagus; RLU, relative light unit; RT–qPCR, real-time quantitative PCR; RQ, relative quantification; UTR, untranslated region; wt, wild type.
