Expression profiling of liposarcoma yields a multigene predictor of patient outcome and identifies genes that contribute to liposarcomagenesis

Abstract

Liposarcomas are the most common type of soft tissue sarcoma but their genetics are poorly defined. To identify genes that contribute to liposarcomagenesis and serve as prognostic candidates, we undertook expression profiling of 140 primary liposarcoma samples, which were randomly split into training set (n = 95) and test set (n = 45). A multigene predictor for distant recurrence-free survival (DRFS) was developed by the supervised principal component method. Expression levels of the 588 genes in the predictor were used to calculate a risk score for each patient. In validation of the predictor in the test set, patients with low risk score had a 3-year DRFS of 83% versus 45% for high risk score patients (P = 0.001). The HR for high versus low score, adjusted for histologic subtype, was 4.42 (95% CI, 1.26-15.55; P = 0.021). The concordance probability for risk score was 0.732. In contrast, the concordance probability for histologic subtype, which had been considered the best predictor of outcome in liposarcoma, was 0.669. Genes related to adipogenesis, DNA replication, mitosis, and spindle assembly checkpoint control were all highly represented in the multigene predictor. Three genes from the predictor, TOP2A, PTK7, and CHEK1, were found to be overexpressed in liposarcoma samples of all five subtypes and in liposarcoma cell lines. RNAi-mediated knockdown of these genes in liposarcoma cell lines reduced proliferation and invasiveness and increased apoptosis. Taken together, our findings identify genes that seem to be involved in liposarcomagenesis and have promise as therapeutic targets, and support the use of this multigene predictor to improve risk stratification for individual patients with liposarcoma.

Figure 1

Kaplan-Meir curves of distant-recurrence–free survival among patients with liposarcoma according to score in the 11-gene predictor, dichotomized at the median. A, patients in the training set. B, patients in the test set.

Figure 2

Kaplan-Meir analysis of distant-recurrence–free survival in the training set according to gene expression. A, TOP2A expression; B, PTK7 expression; C, CHEK1 expression.

Figure 3

Effects of TOP2A, PTK7, and CHEK2 knockdown in ASCs and liposarcoma cell lines. A, Cell proliferation following shRNA knockdown relative to SCR at day 6 after infection. B, Apoptosis at day 6 after infection, assessed by the percentage of cells staining for annexin V. C, Percentage invasion of liposarcoma cell lines at day 2 after lentivirus infection.