Interpretation of somatic POLE mutations in endometrial carcinoma.

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 EC 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 > 100mut/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 EC, and the 6 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 EC. In a pooled analysis of 3,361 EC, 13 EC 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 EC. Additionally, 14 cases with non-pathogenic POLE EDM and MMRd/MSI-H had 5-year RFS of 76.2%, similar to MMRd/MSI-H, POLE wild-type EC, suggesting these should be categorised as MMRd, rather than POLE-ultramutated EC for prognostication. This work provides guidance on classification of EC with POLE mutations, facilitating implementation of POLE testing in routine clinical care. This article is protected by copyright. All rights reserved.