SLFN11 Is a Transcriptional Target of EWS-FLI1 and a Determinant of Drug Response in Ewing Sarcoma

Abstract

Purpose SLFN11 was identified as a critical determinant of response to DNA targeted therapies by analyzing gene expression and drug sensitivity of NCI-60 and CCLE datasets. However, how SLFN11 is regulated in cancer cells remained unknown. Ewing’s sarcoma (ES), which is characterized by the chimeric transcription factor EWS-FLI1, has notably high SLFN11 expression, leading us to investigate whether EWS-FLI1 drives SLFN11 expression and the role of SLFN11 in the drug response of ES cells. Experimental Design Binding sites of EWS-FLI1 on the SLFN11 promoter were analyzed by chromatin immunoprecipitation-DNA sequence (ChIP-Seq) and promoter-luciferase reporter analyses. The relationship between SLFN11 and EWS-FLI1 were further examined in EWS-FLI1-knockdown or -overexpressing cells and in clinical tumor samples. Results EWS-FLI1 binds near the transcription start site of SLFN11 promoter and acts as a positive regulator of SLFN11 expression in ES cells. EWS-FLI1-mediated SLFN11 expression is responsible for high sensitivity of ES to camptothecin and combinations of PARP inhibitors with temozolomide. Importantly, ES patients with higher SLFN11 expression showed better tumor-free survival rate. The correlated expression between SLFN11 and FLI1 extends to leukemia, pediatric, colon, breast and prostate cancers. In addition, expression of other ETS members correlates with SLFN11 in NCI-60 and CCLE datasets, and molecular experiments demonstrate that ETS1 acts as a positive regulator for SLFN11 expression in breast cancer cells. Conclusions Our results imply the emerging relevance of SLFN11 as an ETS transcription factor response gene and for therapeutic response to topoisomerase I inhibitors and temozolomide-PARP inhibitor combinations in ETS-activated cancers.

Resistance to PARP inhibitors by SLFN11 inactivation can be overcome by ATR inhibition

“…Additionally, we tested two Ewing's sarcoma cell lines, EW8 and A673 with high SLFN11 transcripts [25, 26]. SLFN11 protein levels were consistent with transcript levels (Figure 1B).…”

Chemosensitive Relapse in Small Cell Lung Cancer Proceeds through an EZH2-SLFN11 Axis

“…To identify recurrently differentially expressed genes, we generated a meta p value for each gene based on the degree of differential expression in each of the individual models (Figure 3B). Schlafen family member 11 ( SLFN11 ), a gene that we and others have reported as being critical to sensitivity to DNA damaging agents (Barretina et al, 2012; Lok et al, 2016; Sousa et al, 2015; Stewart et al, 2014; Tang et al, 2015; Zoppoli et al, 2012), was among the most significantly downregulated genes. Cancer-testis antigens, a family of genes that are highly sensitive to epigenetic perturbation (De Smet et al, 1999), were significantly upregulated, as well as Twist family bHLH transcription factor 1 ( TWIST1 ), a gene previously described to play an important role in acquired resistance to a variety of agents (Fischer et al, 2015; Zheng et al, 2015).…”

“…We then interrogated the role of SLFN11 in the context of acquired chemoresistance, as it had been previously implicated as a factor regulating DNA damage repair (Mu et al, 2016) and was shown to correlate with responses to DNA damaging agents in vitro (Barretina et al, 2012; Sousa et al, 2015) and in vivo (Tang et al, 2015). SLFN11 is bi-modally expressed when examined across cancer cell lines within the Cancer Cell Line Encyclopedia (CCLE), as well as within SCLC in both primary tumor (Lok et al, 2016) and cell lines (Figure 4A).…”

PARP Inhibitor Activity Correlates with SLFN11 Expression and Demonstrates Synergy with Temozolomide in Small Cell Lung Cancer

“…No such predictive biomarker has been defined for SCLC. Previous in vitro analyses in colon cancer and Ewing sarcoma cell lines have implicated SLFN11 as a correlate of response to conventional DNA damaging agents, including topoisomerase poisons and cisplatin (25, 44, 45). In this study, we substantially expand our knowledge of SLFN11 by showing for the first time that SLFN11 is a strong predictor of SCLC sensitivity to PARP inhibitors, and confirm these findings in vivo through multiple PDX models.…”