Integrated genomic profiling of endometrial carcinoma associates aggressive tumors with indicators of PI3 kinase activation

Abstract

Although 75% of endometrial cancers are treated at an early stage, 15% to 20% of these recur. We performed an integrated analysis of genome-wide expression and copy-number data for primary endometrial carcinomas with extensive clinical and histopathological data to detect features predictive of recurrent disease. Unsupervised analysis of the expression data distinguished 2 major clusters with strikingly different phenotypes, including significant differences in disease-free survival. To identify possible mechanisms for these differences, we performed a global genomic survey of amplifications, deletions, and loss of heterozygosity, which identified 11 significantly amplified and 13 significantly deleted regions. Amplifications of 3q26.32 harboring the oncogene PIK3CA were associated with poor prognosis and segregated with the aggressive transcriptional cluster. Moreover, samples with PIK3CA amplification carried signatures associated with in vitro activation of PI3 kinase (PI3K), a signature that was shared by aggressive tumors without PIK3CA amplification. Tumors with loss of PTEN expression or PIK3CA overexpression that did not have PIK3CA amplification also shared the PI3K activation signature, high protein expression of the PI3K pathway member STMN1, and an aggressive phenotype in test and validation datasets. However, mutations of PTEN or PIK3CA were not associated with the same expression profile or aggressive phenotype. STMN1 expression had independent prognostic value. The results affirm the utility of systematic characterization of the cancer genome in clinically annotated specimens and suggest the particular importance of the PI3K pathway in patients who have aggressive endometrial cancer.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.

Results of unsupervised clustering of expression data from 57 endometrial carcinomas. (A) Two major clusters are identified and recapitulated using the displayed predictor set of 29 genes. Features associated with each tumor are displayed in the bottom 3 panels. PI3K scores in the top tertile are called positive. (B) The ability of the 29 predictor genes to distinguish cluster 1 and 2 tumors was validated in these tumors by quantitative RT-PCR. (C) Recurrence-free survival was significantly lower for patients in cluster 2. Four tumors (all in cluster 2) were metastatic at presentation and omitted from this analysis.

Fig. 2.

Significant copy-number alterations in endometrial cancer. (A) Amplifications (red) and deletions (blue), determined by segmentation analysis of normalized signal intensities from 100K SNP arrays (see Methods), are displayed across the genome (chromosome positions, indicated along the y axis, are proportional to marker density) for 76 tumors and 9 cell lines. (B) GISTIC analysis of copy-number changes. The G score represents the frequency times average amplitude of the aberrations identified in (A). The false discovery rate q-values, representing the statistical significance associated with these scores (7), are displayed along the bottom. Regions with q-values < 0.25 (green lines) were considered significantly altered. The locations of the peak regions of maximal copy-number change and the known cancer-related genes within those peaks are indicated to the right of each panel.

Fig. 3.

Relations between PIK3CA amplification, PI3K activation, and survival. (A) Amplification of a region in 3q26 that includes PIK3CA is significantly associated with poor recurrence-free survival. These amplifications are associated with (B) overexpression of PIK3CA and (C) increased PI3K scores. (D) Among the broader set of poor-prognosis tumors in expression cluster 2, PI3K scores are equally high among tumors without 3q26 amplification and with 3q26 amplification, suggesting alternative methods of pathway activation. (E) Tumors with elevated protein expression of the PI3K pathway member STMN1 had significantly poorer survival, after controlling for age, FIGO stage, histologic subtype, and grade.