Molecular stratification of endometrioid ovarian carcinoma predicts clinical outcome

Abstract

Endometrioid ovarian carcinoma (EnOC) demonstrates substantial clinical and molecular heterogeneity. Here, we report whole exome sequencing of 112 EnOC cases following rigorous pathological assessment. We detect a high frequency of mutation in CTNNB1 (43%), PIK3CA (43%), ARID1A (36%), PTEN (29%), KRAS (26%), TP53 (26%) and SOX8 (19%), a recurrently-mutated gene previously unreported in EnOC. POLE and mismatch repair protein-encoding genes were mutated at lower frequency (6%, 18%) with significant co-occurrence. A molecular taxonomy is constructed, identifying clinically distinct EnOC subtypes: cases with TP53 mutation demonstrate greater genomic complexity, are commonly FIGO stage III/IV at diagnosis (48%), are frequently incompletely debulked (44%) and demonstrate inferior survival; conversely, cases with CTNNB1 mutation, which is mutually exclusive with TP53 mutation, demonstrate low genomic complexity and excellent clinical outcome, and are predominantly stage I/II at diagnosis (89%) and completely resected (87%). Moreover, we identify the WNT, MAPK/RAS and PI3K pathways as good candidate targets for molecular therapeutics in EnOC.

Fig. 1. Flow diagram identifying endometrioid ovarian carcinoma cases for whole exome sequencing.

IHC immunohistochemistry, WES whole exome sequencing, EnOC endometrioid ovarian carcinoma, WT1 Wilms’ tumour 1, QC quality control.

Fig. 2. Unsupervised clustering of endometrioid ovarian carcinomas by patterns of mutation.

Product-moment correlation scores between samples were calculated using binary matrices representing the status of most frequently mutated genes (1 = mutant, 0 = wild-type), yielding a matrix of quantified genomic correlation. These data were subject to hierarchical clustering using Euclidean distance and Ward’s linkage. Bars denote mutation in CTNNB1 and TP53.

Fig. 3. Genomic characterisation of endometrioid ovarian carcinoma (EnOC).

a Whole exome sequencing identifies three major genomic subtypes of endometrioid ovarian carcinoma based on TP53 and CTNNB1 mutation status. Molecular signatures for each tumour are plotted as the fraction of transversions and transitions. Mutations are displayed as an oncoplot. Grey denotes no mutation. Upper plot shows the six most frequently mutated genes; lower plot shows select genes of interest. b Lollipop plots of five common gene targets of mutation. c Mismatch repair (MMR) mutations across cases. d Relationship between tumour mutational burden (TMB) and mutations in POLE and/or MMR genes. Ti transition, tv transversion, MSI microsatellite instability, RD residual disease.

Fig. 4. Genomic complexity of endometrioid ovarian carcinomas (EnOC).

a Representative examples of variant allele frequency density plots for a high complexity tumour (left), intermediate complexity tumour (centre) and low complexity tumour (right). Variant allele frequency (VAF) clusters are shown and summarised within box plots above the density plot; boxes represent the 1st to 3rd quartile, with the median labelled as the central line, and whiskers extend to the data range from 1st and 3rd quartile +/−1.5 times the interquartile range. b Mutant-allele tumour heterogeneity (MATH) genomic complexity scores across all 112 endometrioid ovarian carcinoma (EnOC) cases, ranked high to low. c MATH genomic complexity scores across the three EnOC subtypes. Comparisons were made using the two-sided Mann–Whitney U-test without adjustment for multiple testing (P < 0.0001 and P = 0.0353). m mutant, wt wild-type.

Fig. 5. Genomic subtypes of endometrioid ovarian carcinoma demonstrate distinct clinical behaviour.

a Disease-specific survival based on TP53m and CTNNB1m status; labelled hazard ratio represents comparison of the TP53wt/CTNNB1m group with the TP53m group. HR for TP53wt/CTNNB1wt vs. TP53m = 0.37, 95% CI 0.18–78; HR for TP53wt/CTNNB1m vs. TP53wt/CTNNB1wt = 0.31, 95% CI 0.11–0.88. b Summary of the PRISTINE algorithm for molecular subtyping in endometrioid ovarian carcinoma. m mutant, wt wild-type, RD residual disease, WES whole exome sequencing, DSS disease-specific survival.