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.
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