Somatic mutation profiles of clear cell endometrial tumors revealed by whole exome and targeted gene sequencing

Authors

Matthieu Le Gallo

Meghan L. Rudd

Mary Ellen Urick

Nancy F. Hansen

Suiyuan Zhang

Fred Lozy

Dennis C. Sgroi

August Vidal Bel

Xavier Matias-Guiu

Russell R. Broaddus

Karen H. Lu

Douglas A. Levine

David G. Mutch

Paul J. Goodfellow

Helga B. Salvesen

James C. Mullikin

Daphne W. Bell

Doi

10.1002/cncr.30745

PMID: 28485815 · DOI: 10.1002/cncr.30745 · Journal: Cancer (2017)

TL;DR

Le Gallo et al. performed whole-exome sequencing of 16 paired tumor-normal clear cell endometrial carcinoma (CCEC) samples and Sanger-sequenced 22 genes-of-interest in another 47 CCECs (total n=63), the largest exome-scale interrogation of this rare, high-grade endometrial cancer subtype to date (PMID:28485815). They confirmed frequent mutations in TP53 (39.7%), PIK3CA (23.8%), PIK3R1 (15.9%), ARID1A (15.9%), PPP2R1A (15.9%), and SPOP (14.3%); microsatellite instability was present in 11.3% of cases. They nominate TAF1 (mutated in 9.5%) and KMT2C (MLL3, 7.9%) as novel candidate CCEC driver genes, and show CCECs are molecularly heterogeneous, with subsets resembling either uterine serous (USC) or endometrioid (UEC) endometrial carcinomas.

Cohort & data

  • 63 clinically diagnosed clear cell endometrial carcinoma (UCCC) cases — 59 pure CCEC plus 4 mixed-histology endometrial cancers (UCEC) for which only the CCEC component was sequenced (PMID:28485815).
  • Discovery screen: 16 paired tumor-normal DNAs subjected to whole-exome sequencing (13 pairs Illumina Truseq capture, 3 pairs Agilent SureSelect; mean depth 75x; 89.3% of targeted bases at sufficient coverage) (PMID:28485815).
  • Prevalence screen: Sanger sequencing of 22 genes-of-interest in another 47 CCECs (PMID:28485815).
  • Microsatellite instability assessed by genotyping five mononucleotide repeats (msi-pcr-pentaplex); MSI-high (≥2 unstable markers) reported as MSI; MSI-low/-negative reported as MSS (PMID:28485815).
  • Reads aligned to NCBI Build 36 (hg18) using CASAVA v1.8.0 + cross_match (banded Smith-Waterman); variants called with bam2mpg, filtered with VarSifter (MPG ≥10 normal, MPV ≥10 tumor, ≥5 reads/site) (PMID:28485815).
  • Missense functional impact predicted with SIFT, Mutation Assessor, and PolyPhen-2; calls flagged as functional if ≥2 algorithms scored damaging (PMID:28485815).
  • Raw exome data deposited at dbGaP accession phs000967.v1.p1; cBioPortal study id [uccc_nih_2017](../datasets/uccc_nih_2017.md) (PMID:28485815).

Key findings

  • Two of 16 exomes (T61, T77) were MSI with high mutational loads (662 and 472 somatic variant calls). The 14 MSS exomes had low loads (7–85 calls), totalling 236 validated nonsynonymous or splice-junction somatic mutations across 222 protein-encoding genes (validation rate 77.1%, 236/306 attempted) (PMID:28485815).
  • Across all 63 CCECs the most frequently mutated genes-of-interest were TP53 (39.7%), PIK3CA (23.8%), PIK3R1 (15.9%), ARID1A (15.9%), PPP2R1A (15.9%), SPOP (14.3%), TAF1 (9.5%), FBXW7 (7.9%), and MLL3/KMT2C (7.9%); MSI in 11.3% (PMID:28485815).
  • TAF1 is nominated as a novel candidate CCEC driver: 6/63 (9.5%) tumors carried 8 missense mutations; 5 mutations localized to the putative histone acetyltransferase (HAT) domain, including two recurrently mutated residues Arg843 and Ala850. The other 3 TAF1 mutations (Val405Met, Arg1163Cys, Arg1198Gln) all occurred in a single hypermutated MSH6-mutant tumor (T113). All 8 TAF1 mutations are predicted to be functional by ≥2 of 3 in silico algorithms (PMID:28485815).
  • KMT2C (MLL3) is also a novel CCEC candidate driver: 6 mutations in 5 tumors (3 frameshifts, 3 missense). Each frameshift occurred N-terminal to the SET domain, consistent with loss-of-function (PMID:28485815).
  • Cross-histology comparison using 7 differentially mutated genes (TP53, PPP2R1A, PTEN, ARID1A, KRAS, PIK3R1, PIK3CA) plus MSI: 66.7% of CCECs, 82.2% of USC (n=45), and 97.5% of UEC (n=40) had ≥1 alteration. CCEC mutation profiles distributed 27.0% serous-like (group 1), 19.1% mixed (group 2), 20.6% endometrioid-like (group 3), and 33.3% with no detectable alterations — an intermediate distribution between SECs (75.5% group 1 or 2) and EECs (82.5% group 3) (PMID:28485815).
  • The PI3-Kinase axis (PIK3CA–PIK3R1–PTEN) was mutated in 34.9% of CCEC cases (PMID:28485815).
  • No POLE exonuclease-domain hotspot mutations were identified among the CCECs; one tumor (T24) had a non-hotspot POLE exonuclease frameshift (Phe367Leufs*15) but did not exhibit an ultramutated phenotype (PMID:28485815).

Genes & alterations

Clinical implications

  • 11.3% of CCECs are MSI, raising the possibility that this subset could respond to anti-PD-1 therapy: the authors note clinical responses of two MSI EC patients to pembrolizumab in a phase 2 trial of mismatch-repair-deficient tumors (PMID:28485815).
  • 34.9% of CCECs harbor mutations in the druggable PI3-Kinase pathway (PIK3CA–PIK3R1–PTEN), implying potential vulnerability to PI3K/AKT/mTOR-axis inhibitors (PMID:28485815).
  • The observed molecular heterogeneity within clinically diagnosed CCEC supports the value of molecular (not purely morphologic) subclassification of high-grade endometrial cancer and is consistent with the TCGA UCEC four-subgroup framework (POLE-ultramutated, MSI-hypermutated, copy-number-low MSS, copy-number-high serous-like) (PMID:28485815).
  • Absence of POLE-exonuclease hotspots in CCEC contrasts with their favorable-prognosis association in EECs (PMID:28485815).

Limitations & open questions

  • No systematic central pathology re-review of discovery or prevalence cases. Given documented interobserver variability in distinguishing CCEC from high-grade EEC and SEC (k values 0.18–0.69 across multiple studies), some “molecular heterogeneity” may reflect histologic misclassification rather than true biological diversity (PMID:28485815).
  • Reads aligned to hg18 (NCBI Build 36) — older reference genome build than current standards (GRCh37/38), potentially limiting downstream comparability (PMID:28485815).
  • 33.3% of CCECs had no detectable alteration across the 7-gene + MSI panel, suggesting additional driver events outside the surveyed loci remain to be discovered (PMID:28485815).
  • TAF1 and KMT2C are nominated as candidate drivers based on mutation prevalence and predicted functional impact only; functional validation (loss-of-function assays, mouse models) was not performed in this study (PMID:28485815).
  • Discovery cohort (n=16 exomes) is modest by current standards; copy-number and structural variation were not systematically characterized (PMID:28485815).

Citations from this paper used in the wiki

  • “Among the 63 CCECs in this study, we identified frequent somatic mutations in TP53 (39.7%), PIK3CA (23.8%), PIK3R1 (15.9%), ARID1A (15.9%), PPP2R1A (15.9%), SPOP (14.3%), and TAF1 (9.5%), as well as MSI (11.3%).” — Abstract, Results.
  • “Five of eight mutations in TAF1, a gene with no known role in CCEC, localized to the putative histone acetyltransferase domain and included two recurrently mutated residues.” — Abstract.
  • “All eight TAF1 mutations are predicted to impact function by at least two of three in silico algorithms.” — Results.
  • “The PIK3CA-PIK3R1-PTEN axis of the druggable PI3-Kinase pathway was mutated in 34.9% of cases. MSI was present in 11.3% of cases and is noteworthy given the clinical responses of two MSI EC patients to the anti-PD-1 antibody pembrolizumab in a phase 2 trial.” — Discussion.
  • “Our finding that 39.7% of 63 CCECs in our study were TP53-mutated and another 11.3% had MSI further demonstrates that the molecular features of CCECs are heterogeneous and overlap with those of SECs and EECs.” — Discussion.
  • “POLE exonuclease domain hotspot mutations, which are associated with a favorable outcome in EECs, were not present among the CCECs in our study.” — Discussion.

This page was processed by crosslinker on 2026-05-15.