Genomic signatures predict poor outcome in undifferentiated pleomorphic sarcomas and leiomyosarcomas

Abstract

Undifferentiated high-grade pleomorphic sarcomas (UPSs) display aggressive clinical behavior and frequently develop local recurrence and distant metastasis. Because these sarcomas often share similar morphological patterns with other tumors, particularly leiomyosarcomas (LMSs), classification by exclusion is frequently used. In this study, array-based comparative genomic hybridization (array CGH) was used to analyze 20 UPS and 17 LMS samples from untreated patients. The LMS samples presented a lower frequency of genomic alterations compared with the UPS samples. The most frequently altered UPS regions involved gains at 20q13.33 and 7q22.1 and losses at 3p26.3. Gains at 8q24.3 and 19q13.12 and losses at 9p21.3 were frequently detected in the LMS samples. Of these regions, gains at 1q21.3, 11q12.2-q12.3, 16p11.2, and 19q13.12 were significantly associated with reduced overall survival times in LMS patients. A multivariate analysis revealed that gains at 1q21.3 were an independent prognostic marker of shorter survival times in LMS patients (HR = 13.76; P = 0.019). Although the copy number profiles of the UPS and LMS samples could not be distinguished using unsupervised hierarchical clustering analysis, one of the three clusters presented cases associated with poor prognostic outcome (P = 0.022). A relative copy number analysis for the ARNT, SLC27A3, and PBXIP1 genes was performed using quantitative real-time PCR in 11 LMS and 16 UPS samples. Gains at 1q21-q22 were observed in both tumor types, particularly in the UPS samples. These findings provide strong evidence for the existence of a genomic signature to predict poor outcome in a subset of UPS and LMS patients.

Figure 1. Overall survival curves from LMS patients with specific genomic alterations.

Gains at (A) 1q21.3, (B) 11q12.2-q12.3, (C) 16p11.2, and (D) 19q13.12 were associated with shorter survival times. P-values were determined using the Log-rank test.

Figure 2. Unsupervised hierarchical clustering of 20 undifferentiated pleomorphic sarcomas (UPSs) and 17 leiomyosarcomas (LMSs).

(A) In the dendrogram, cluster 1 is shown in green, cluster 2 is shown in blue, and cluster 3 is shown in red. Clusters related to the sites of anatomical origin were not observed for these tumors; origin sites include the following regions: upper extremity (pink), lower extremity (purple), trunk (orange), retroperitoneum (yellow), and head and neck (rose). (B) Genomic alterations were detected in clusters 1 (C1; 11 cases), 2 (C2; 16 cases), and 3 (C3; 10 cases). The top bars (blue) indicate genetic gains, whereas the lower bars (red) indicate genetic losses. The images shown were adapted from the output of the Nexus 6.0 software program.

Figure 3. Quantification of DNA copy number alterations using qPCR for the ARNT, PBXIP1, SLC27A3, and CCND1 genes.

Eight primer pairs were designed, including (A) three for ARNT (ARNT-P1, ARNT-P2, and ARNT-P3); (B) two for PBXIP1 (PBXIP1-P1 and PBXIP1-P2) and one for SLC27A3 (SLC27A3-P1); and (C) two for CCND1 (CCND1-P1 and CCND1-P2).