Interpretation of somatic POLE mutations in endometrial carcinoma

Abstract

Pathogenic somatic missense mutations within the DNA polymerase epsilon (POLE) exonuclease domain define the important subtype of ultramutated tumours ('POLE-ultramutated') within the novel molecular classification of endometrial carcinoma (EC). However, clinical implementation of this classifier requires systematic evaluation of the pathogenicity of POLE mutations. To address this, we examined base changes, tumour mutational burden (TMB), DNA microsatellite instability (MSI) status, POLE variant frequency, and the results from six in silico tools on 82 ECs with whole-exome sequencing from The Cancer Genome Atlas (TCGA). Of these, 41 had one of five known pathogenic POLE exonuclease domain mutations (EDM) and showed characteristic genomic alterations: C>A substitution > 20%, T>G substitutions > 4%, C>G substitutions < 0.6%, indels < 5%, TMB > 100 mut/Mb. A scoring system to assess these alterations (POLE-score) was developed; based on their scores, 7/18 (39%) additional tumours with EDM were classified as POLE-ultramutated ECs, and the six POLE mutations present in these tumours were considered pathogenic. Only 1/23 (4%) tumours with non-EDM showed these genomic alterations, indicating that a large majority of mutations outside the exonuclease domain are not pathogenic. The infrequent combination of MSI-H with POLE EDM led us to investigate the clinical significance of this association. Tumours with pathogenic POLE EDM co-existent with MSI-H showed genomic alterations characteristic of POLE-ultramutated ECs. In a pooled analysis of 3361 ECs, 13 ECs with DNA mismatch repair deficiency (MMRd)/MSI-H and a pathogenic POLE EDM had a 5-year recurrence-free survival (RFS) of 92.3%, comparable to previously reported POLE-ultramutated ECs. Additionally, 14 cases with non-pathogenic POLE EDM and MMRd/MSI-H had a 5-year RFS of 76.2%, similar to MMRd/MSI-H, POLE wild-type ECs, suggesting that these should be categorised as MMRd, rather than POLE-ultramutated ECs for prognostication. This work provides guidance on classification of ECs with POLE mutations, facilitating implementation of POLE testing in routine clinical care. © 2019 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.

Keywords: POLE; endometrial cancer; molecular classification.

Figure 1

Mutational features of EC with POLE variants in the TCGA. The colour scheme for the mutation type is on the right of the histogram. Cases are grouped by mutations, with the most frequent POLE mutations in first place. The COSMIC 10 signature contribution, the points obtained in the POLE pathogenicity score (POLE‐score), the recurrence of the variant in EC, microsatellite instability (MSI) status, and POLE domain mutated are colour‐coded (legend on the right of the histogram). Below are the cases without POLE mutations; two rows depict the median plus standard deviation of the base change proportions and tumour mutation burden (TMB) of MSI‐H and MSS ECs without a POLE mutation in the TCGA.

Figure 2

POLE genomic alteration score (POLE‐score). Diagnostic scoring system based on mutation type proportion and TMB of the five hotspot POLE mutations, as well as the variant recurrence.

Figure 3

Clinical outcome of MMRd–POLEmut ECs. Kaplan–Meier survival curves for RFS (A) and OS (B) of MMRd–POLEmut ECs. RFS and OS of MMRd–POLEmut ECs with a pathogenic POLE EDM (mutation present in Table 3) versus all other tumours MMRd–POLEmut (C and D).