Fig. 4: Genomic alterations vulnerable to existing treatment options in Chinese ACGEJ in comparison with TCGA ACGEJ. | Nature Communications

Fig. 4: Genomic alterations vulnerable to existing treatment options in Chinese ACGEJ in comparison with TCGA ACGEJ.

From: Genomic and transcriptomic alterations associated with drug vulnerabilities and prognosis in adenocarcinoma at the gastroesophageal junction

Fig. 4

a Chemotherapeutic agents predicted to be responsive in Chinese ACGEJ. Left panel shows genomic alterations vulnerable to each chemotherapeutic agent and right panel shows the percentage of samples responsive to each chemotherapeutic agent, with comparisons between our ACGEJ patient set and the TCGA ACGEJ dataset. b Bar plots comparing ACGEJ samples likely responsive and unresponsive to Anthracyclines, Gemcitabine, or Mytomycin C (n = 91 and 33, respectively) for the frequencies of WGD, chromothripsis, and kataegis (Fisher’s exact tests). c Genomic alterations in our ACGEJ samples and the corresponding targeted therapeutic agents. Only genomic alterations detected in ≥5 samples and agents having potential targets in ≥20% samples are shown. d Percentage of samples predicted to be responsive to different targeted therapeutic agents, with comparisons between our patients and TCGA patients without ERBB2 amplification (n = 89 and 85, respectively). Only agents with potential targets in ≥20% of our patients or TCGA patients are shown. e Comparison between likely druggable and undruggable ACGEJ samples (n = 113 and 11, respectively) for TMB, chromosomal (Chr.) arm or gene level CNVs (two-sided Wilcoxon rank-sum tests), and the frequencies of WGD (Fisher’s exact test). f In vitro validation of predicted vulnerabilities to chemotherapeutic and targeted therapeutic agents. Box plots compare relative viability (expressed as OD450 value) of different cell lines, likely vulnerable (blue) or invulnerable (red) to specified therapeutic agents, after treatment with optimal dose (in parentheses) of corresponding agents for 72 h. Each dot represents the result of one independent experiment and each experiment had three replicates on one cell line; n represents the number of cell lines; P values derived from two-sided Wilcoxon rank-sum tests. Box plots in (e, f) show the median (central line), the 25–75% interquartile range (IQR) (box limits), the ±1.5 times IQR (Tukey whiskers), and all data points, among which the lowest and the highest points indicate minimal and maximal values, respectively.

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