Metastatic and recurrent adrenocortical cancer is not defined by its genomic landscape

Fig. 1. a Frequency of copy number gains/losses in 17 of the 25 ACC tumors with paired normal DNA. The y-axis represents the percentage of samples with gain/loss.[ngCGH + Nexus segmentation]. Eight tumors removed due to excess noise. b Mutational Signature in 25 samples from Tumor/Normal pairs and in 18 samples with Tumor Only analysis

Fig. 2. Mutations in individual patients. Genes that were mutated in \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\ge$$\end{document}≥ 4 patients (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\ge$$\end{document}≥ 9%) and validated by a second sequencing method are shown. Column labeled H, depicts the results in the H295 cell line. Top portion: Mutations found in \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\ge$$\end{document}≥ 9% of those samples with buffy coats; Lower portion: Mutations found in \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy}…

Fig. 3. a ACC mutation frequencies. The heat map lists the frequencies of the 38 most commonly mutated genes across 3 ACC studies: COMETE (n = 45, cutoff = 4) [16], TCGA (n = 91, cutoff = 9) [8], and NIH (n = 43, cutoff = 7 [the current study]), as well as the average percentage of the three studies (ACC column, n = 179), and the cancer average as recorded in the TCGA PanCancerAtlas, which includes 33 cancers and 11.315 cases [https://gdc.cancer.gov/]. The heat map is sorted according to the average percentage of the three studies – the ACC column (i.e. number of patients with the mutation / total number of patients). The four genes shown in italic bold on shaded background (TP53, CTNNB1, NF1 and AFF1) are included in the 576 COSMIC Cancer Gene Census (CGC) Tier 1 genes, while the three genes in bold also on a shaded background (MUC16, MUC4 and PABPC1) are among the 147 CGC Tier 2 genes [REF.: COSMIC, Catalogue of Somatic Mutations in Cancer, https://cancer.sanger.ac.uk/cosmic]. b Correlation between the mutation frequency of the 38 cancer genes in 3A in ACC and in cancer in general both plotted as the average of their occurrence in ACC (Y-axis) and all cancers (X-axis). The diagonal…

Fig. 4. a Kaplan Meier plots evaluating the impact of TP53 and CTNNB1 mutation on overall survival in the TCGA and in the NIH datasets. These can be compared to the Kaplan Meier plots derived from gene expression array data for aggressive C1A and indolent C1B subtypes [6, 8]. b Total number of mutations for each subgroup are graphically depicted with the mean and SD. The numbers in brackets below each dotplot are the mean number of mutations for that subgroup. Mutation counts in the ACC TCGA dataset are higher in tumors harboring a TP53 MUT compared to those with TP53WT [***p = 0.001], although many of those patients were also noted to have mutations suggestive of MMR deficiency (red symbols). The correlation with TP53 MUT was weaker in the smaller NIH dataset [*p = 0.05]. Orange symbols indicate that the mutation counts were additionally filtered by germline sequencing in those patients. None of the patients in the NIH set had germline TP53 mutations

Fig. 5. Results of cDNA Array analysis of ACC gene expression. a Heat-map and unsupervised hierarchical clustering based on the 769 genes that differ most between ACC and NA (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\sigma /\sigma \mathrm{max}$$\end{document}σ/σmax >0.2, p < 0.05, q = 0.18, > 2-FC, one sample per patient, probe-sets collapsed to median per gene). Compared to the normal adrenal, 289 DEG were noted to be upregulated, and 480 downregulated in the tumors. The ACC samples cluster separately from the normal adrenal (NA) samples, with the exception of 35 T, 47 T, and 48 T (gray arrow) that cluster together with the NA samples (Note: as these tumor samples were from metastasectomies normal adrenal tissue could not have contaminated the samples). b Heat-map and unsupervised hierarchical clustering based on the 33 out of 576 Tier 1 COSMIC cancer census genes that differ the most between ACC and NA (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts}…