Fig. 2: Tumor mutational burden (TMB), microsatellite instability (MSI) and ATRX/TERT alterations in mPPGLs.

The data included correspond to 261 tumor-normal pairs from the CNIO and TCGA cohorts. a Overview of the number of variants, MSI score, and other clinical and genomic features of the whole series. Tumors have been ranked by TMB (calculated with category 5 variants). The legend in the bottom indicates the color code for each item. The filtering strategy for WES events is shown in Supplementary Fig. 2. b TMB and c MSI score (extracted with MANTIS) across PPGL tumors (n = 256). P-values were calculated with a two-sided Mann–Whitney–Wilcoxon (MWW) test and significant ones are shown in the figures. d Correlation between TMB and MSI score. Two-sided Pearson’s correlation coefficient is shown. e, f Progression-free survival analysis of patients according to primary tumors’ TMB and MSI score, respectively. Only primary tumors from non-metastatic and metastatic patients were analyzed. Higher TMB indicates tumors with values > than the third quartile (n = 37); lower TMB for the remainder cases (n = 175). Higher MSI score indicates cases with MSI score >0.15 (n = 40); lower MSI for the remainder cases (n = 172). Kaplan–Meier plots of time to progression (time between the first PPGL diagnosis and the first documented metastasis) are shown together with P-values calculated using a log-rank test. Median progression time (± standard error) of each group is depicted in the corresponding color. Patients without evidence of metastases were censored at the date of the last follow-up. g–i TMB variation according to tumor volume (cm³) (n = 28), % Ki67 positive cells (n = 16) and MKI67 mRNA expression (n = 191). Volumes and % Ki67 cells data, when available, were extracted from the pathological anatomy reports received with each specimen. High MKI67 mRNA expression indicates expression levels above the 3rd quartile value of the whole cohort and low MKI67 mRNA expression when levels were beneath the 3rd quartile value. j TMB variation according to the age of the patient at surgery (n = 225). For (h)–(k) a two-sided MWW was applied to test for differences, and, except for (j), only primary tumors (non-metastatic, aggressive and metastatic) were considered. k Frequency of ATRX/TERT-alterations within genomic subtypes. Two-sided Freeman–Halton test was used to test for differences between genomic subtypes. Metastatic tumors include primary tumors and metastases; if paired primary-metastasis is available, only one tumor per patient is represented. l TMB and m MSI score in ATRX/TERT-wild-type (WT) and in ATRX/TERT-altered tumors (n = 256). Two-sided MWW was used to test for differences. For all box-plots in this figure: the median value is marked, and Tukey whiskers are represented. See also Supplementary Fig. 3 and Supplementary Table 2. Source data are provided as a Source Data file.