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  • br In the TCGA study POLE ECs were found to

    2020-07-28


    In the TCGA study, POLE ECs were found to have the best and copy-number high (serous-like) ECs the worst progression-free survival [3]. As a hypothesis-generating analysis, we used the dominant mutational signatures to categorize ECs into i) dominant POLE signatures 10 or 14,
    number high. This stratification was found to be significantly associated with progression-free survival (p = 0.045, log-rank) and recapitulated the survival curves based on the molecular subtypes reported by TCGA [3] (Supplementary Fig. 1b).
    3.2. POLE EDM type and POLE mutational signatures
    Of the 17 cases within the POLE (ultramutated) molecular subtype, all of which harbored a POLE EDM, 13 ECs displayed a dominant signa-ture 10 associated with POLE mutations, one a dominant aging-related signature 1, one a dominant DNA MMR signature 6, and two ECs had a dominant signature 14 (Fig. 1b). In the latter two cases, co-occurrence of POLE EDMs with either MLH1 gene promoter methylation or MSH6 mutations were detected, consistent with the notion that signature 14 is present in tumors with concurrent loss of POLE and MMR function [29,30]. We also observed that the percentage of signature 10 present in a given EC varied according to the specific POLE EDM. ECs with M444K or P286R POLE hotspot EDMs had the highest percentage of mu-tational signature 10 (median 91%, range 87–100%), followed by ECs
    Fig. 1. Mutational signatures of primary endometrioid and serous endometrial cancers stratified according to molecular subtype. A) The dominant mutational signatures of 232 endometrioid and serous endometrial carcinomas from The Cancer Genome Atlas (TCGA) [3] stratified according to molecular subtype. Mutational signatures are color-coded according to the legend on the right, and the number of endometrial cancers displaying a specific dominant mutational signature is shown in each bar. B) The mutational signatures of the 17 endometrial cancers of the 232 endometrioid and serous endometrial cancers studied by TCGA [3] and classified as of POLE (ultramutated) molecular subtype, harboring POLE exonuclease domain mutations, are shown. Cases are sorted by their proportion of signature 10 associated with POLE alterations, and molecular signatures are color-coded according to the legend. Information on the exact POLE exonuclease domain mutation (amino acid), the primary and secondary molecular signatures, the number of non-synonymous single nucleotide variants (SNVs), microsatellite instability (MSIsensor score) and MLH1 promoter methylation is provided for each case on the right. AA, amino Norfloxacin change; EDM, exonuclease domain mutation; MSI, microsatellite instability; MSS, microsatellite stable.
    with V411L mutations (median 74%, range 30–76%). By contrast, the three ECs with POLE EDMs not affecting known hotspots either had a dominant aging-related signature 1 (R305C) or a dominant signature 14 (i.e. S297F and L424I; Fig. 1b). Furthermore, POLE ECs with a domi-nant signature 10 were significantly less likely to be MSI-high, as de-fined by MSISensor, than those with dominant signatures 1, 6 or 14 (8% vs 75% MSI-high, p = 0.02, Fisher's exact test; Fig. 1b) [30]. Of note, we identified one copy-number low (endometrioid) EC with a dominant molecular signature 10 (Fig. 1a; Supplementary Figs. S1 and S3); this case harbored a POLE L424V EDM, a known pathogenic muta-tion associated with familial colonic polyposis and colorectal cancer [31], but not considered to constitute a POLE hotspot mutation in ECs.
    3.3. HR DNA repair defects in copy-number high Norfloxacin (serous-like) ECs
    Nine copy-number high (serous-like) cancers (15%) had a dominant mutational signature 3 associated with defective homologous recombi-nation DNA repair (HRD), and were of endometrioid (n = 3) and serous (n = 6) histologic subtypes. Of the remaining 51 copy-number high (se-rous-like) ECs, ten (10/51; 20%) had a secondary signature 3; of these, seven were of serous, two of endometrioid and one of mixed histologic subtype (Fig. 2).
    Of the nine ECs with a dominant signature 3, six (67%) displayed high LST scores [22], another genomic feature associated with HR defi-ciency. Furthermore, three of these nine ECs, all with high LST scores, harbored bi-allelic pathogenic germline BRCA1 mutations, and were of endometrioid histology (Fig. 2). Also, five ECs with a secondary signa-ture 3 (50%) had high LST scores, however no bi-allelic genetic alter-ations affecting HRD genes were found.
    In the EC study by TCGA [3], it was reported that copy-number high (serous-like) ECs shared many molecular features with both HGSOCs and basal-like breast cancers, and, therefore, some of the treatment par-adigms applicable to these cancers could also be extended to copy-number high (serous-like) ECs. HGSOCs and basal-like breast cancers frequently harbor alterations affecting the HRD pathway [15,16,23]. Mutational signature analysis performed here revealed that 55% of HGSOCs (132/225) [15] and 46% of basal-like breast cancers (67/146) [16] harbored a dominant HRD-related signature 3, as compared to 15% of copy-number high (serous-like) ECs (p b 0.001 and p = 0.007, re-spectively, Fisher's exact test; Fig. 3). Consistent with this observation, other features of defective HRD, including LST scores, the average length of small deletions [24] and bi-allelic genetic alterations in HRD genes were significantly lower in ECs of copy-number high (se-rous-like) molecular subtype than in HGSOCs and basal-like breast