TRIM8 modulates the EWS/FLI oncoprotein to promote survival in Ewing sarcoma

Fusion-transcription factors (fusion-TFs) represent a class of driver oncoproteins that are difficult to therapeutically target. Recently, protein degradation has emerged as a strategy to target these challenging oncoproteins. The mechanisms that regulate fusion-TF stability, however, are generally unknown. Using CRISPR-Cas9 screening, we discovered tripartite motif-containing 8 (TRIM8) as an E3 ubiquitin ligase that ubiquitinates and degrades EWS/FLI, a driver fusion-TF in Ewing sarcoma. Moreover, we identified TRIM8 as a selective dependency in Ewing sarcoma compared with >700 other cancer cell lines. Mechanistically, TRIM8 knockout led to an increase in EWS/FLI protein levels that was not tolerated. EWS/FLI acts as a neomorphic substrate for TRIM8, defining the selective nature of the dependency. Our results demonstrate that fusion-TF protein stability is tightly regulated and highlight fusion oncoprotein-specific regulators as selective therapeutic targets. This study provides a tractable strategy to therapeutically exploit oncogene overdose in Ewing sarcoma and potentially other fusion-TF-driven cancers.

Selective USP7 inhibition elicits cancer cell killing through a p53-dependent mechanism

Ubiquitin specific peptidase 7 (USP7) is a deubiquitinating enzyme (DUB) that removes ubiquitin tags from specific protein substrates in order to alter their degradation rate and sub-cellular localization. USP7 has been proposed as a therapeutic target in several cancers because it has many reported substrates with a role in cancer progression, including FOXO4, MDM2, N-Myc, and PTEN. The multi-substrate nature of USP7, combined with the modest potency and selectivity of early generation USP7 inhibitors, has presented a challenge in defining predictors of response to USP7 and potential patient populations that would benefit most from USP7-targeted drugs. Here, we describe the structure-guided development of XL177A, which irreversibly inhibits USP7 with sub-nM potency and selectivity across the human proteome. Evaluation of the cellular effects of XL177A reveals that selective USP7 inhibition suppresses cancer cell growth predominantly through a p53-dependent mechanism: XL177A specifically upregulates p53 transcriptional targets transcriptome-wide, hotspot mutations in TP53 but not any other genes predict response to XL177A across a panel of ~500 cancer cell lines, and TP53 knockout rescues XL177A-mediated growth suppression of TP53 wild-type (WT) cells. Together, these findings suggest TP53 mutational status as a biomarker for response to USP7 inhibition. We find that Ewing sarcoma and malignant rhabdoid tumor (MRT), two pediatric cancers that are sensitive to other p53-dependent cytotoxic drugs, also display increased sensitivity to XL177A.

Radiation exposure of image-guided intrathecal administration of nusinersen to adult patients with spinal muscular atrophy

PURPOSE

To examine diagnostic reference levels (DRL) and achievable doses (AD) of image-guided and size-specific dose estimates (SSDE) and organ and effective doses of CT-guided intrathecal nusinersen administration to adult patients with spinal muscular atrophy (SMA).

METHODS

This study involved a total of 60 image-guided intrathecal nusinersen treatments between August 2017 and June 2018. Patient cohort comprised 14 adult patients with the following SMA types: type 2 (n = 9) and type 3 (n = 5) with a mean age of 33.6 years (age range 25-57 years). DRL, AD, SSDE, organ, and effective doses were assessed with a dose-monitoring program based on the Monte Carlo simulation techniques.

RESULTS

DRL and AD for computed tomography are summarised as follows: in terms of CT-dose index (CTDI_vol), DRL 56.4 mGy and AD 36.7 mGy; in terms of dose-length product (DLP), DRL 233.1 mGy cm and AD 120.1 mGy cm. DRL and AD for fluoroscopic guidance were distributed as follows: in terms of dose-area product (DAP), DRL 239.1 μGy m² and AD 135.2 mGy cm². Mean SSDE was 9.2 mGy. Mean effective dose of the CT-guided injections was 2.5 mSv (median 2.0 mSv, IQR 1.3-3.2 mSv). Highest organ doses in the primary beam of radiation were the small intestine 12.9 mSv, large intestine 9.5 mSv, and ovaries 3.6 mSv.

CONCLUSION

Radiation exposure of SMA patients measured as DRLs is generally not higher compared with patients without SMA despite severe anatomical hazards. Dose monitoring data may allow clinicians to stratify radiation risk, identify organs at risk, and adopt measures for specific radiation dose reduction.

Resistance to Epigenetic-Targeted Therapy Engenders Tumor Cell Vulnerabilities Associated with Enhancer Remodeling

Drug resistance represents a major challenge to achieving durable responses to cancer therapeutics. Resistance mechanisms to epigenetically targeted drugs remain largely unexplored. We used bromodomain and extra-terminal domain (BET) inhibition in neuroblastoma as a prototype to model resistance to chromatin modulatory therapeutics. Genome-scale, pooled lentiviral open reading frame (ORF) and CRISPR knockout rescue screens nominated the phosphatidylinositol 3-kinase (PI3K) pathway as promoting resistance to BET inhibition. Transcriptomic and chromatin profiling of resistant cells revealed that global enhancer remodeling is associated with upregulation of receptor tyrosine kinases (RTKs), activation of PI3K signaling, and vulnerability to RTK/PI3K inhibition. Large-scale combinatorial screening with BET inhibitors identified PI3K inhibitors among the most synergistic upfront combinations. These studies provide a roadmap to elucidate resistance to epigenetic-targeted therapeutics and inform efficacious combination therapies.

Genome-scale CRISPR-Cas9 screen identifies druggable dependencies in TP53 wild-type Ewing sarcoma

Stolte et al. use genome-scale CRISPR-Cas9 screening technology to identify druggable targets for TP53 wild-type Ewing sarcoma and discover reactivation of p53 through inhibition of MDM2, MDM4, Wip1, or USP7 as therapeutic strategies for the disease.

Ewing sarcoma is a pediatric cancer driven by EWS-ETS transcription factor fusion oncoproteins in an otherwise stable genomic background. The majority of tumors express wild-type TP53, and thus, therapies targeting the p53 pathway would benefit most patients. To discover targets specific for TP53 wild-type Ewing sarcoma, we used a genome-scale CRISPR-Cas9 screening approach and identified and validated MDM2, MDM4, USP7, and PPM1D as druggable dependencies. The stapled peptide inhibitor of MDM2 and MDM4, ATSP-7041, showed anti-tumor efficacy in vitro and in multiple mouse models. The USP7 inhibitor, P5091, and the Wip1/PPM1D inhibitor, GSK2830371, decreased the viability of Ewing sarcoma cells. The combination of ATSP-7041 with P5091, GSK2830371, and chemotherapeutic agents showed synergistic action on the p53 pathway. The effects of the inhibitors, including the specific USP7 inhibitor XL-188, were rescued by concurrent TP53 knockout, highlighting the essentiality of intact p53 for the observed cytotoxic activities.

EWS/FLI Confers Tumor Cell Synthetic Lethality to CDK12 Inhibition in Ewing Sarcoma

Many cancer types are driven by oncogenic transcription factors that have been difficult to drug. Transcriptional inhibitors, however, may offer inroads into targeting these cancers. Through chemical genomics screening, we identified that Ewing sarcoma is a disease with preferential sensitivity to THZ1, a covalent small-molecule CDK7/12/13 inhibitor. The selective CDK12/13 inhibitor, THZ531, impairs DNA damage repair in an EWS/FLI-dependent manner, supporting a synthetic lethal relationship between response to THZ1/THZ531 and EWS/FLI expression. The combination of these molecules with PARP inhibitors showed striking synergy in cell viability and DNA damage assays in vitro and in multiple models of Ewing sarcoma, including a PDX, in vivo without hematopoietic toxicity.

Abstract 2441: CDK12/13 inhibition cooperates with the Ewing sarcoma oncoprotein EWS/FLI to attenuate homologous recombination repair in Ewing sarcoma cells

A therapeutic challenge in pediatric oncology is the paucity of readily “druggable” genetic events in many of the childhood malignancies. These tumors are frequently defined by sentinel abnormalities involving transcription factors in an otherwise quiet genomic landscape. One approach to treating these tumors would involve direct targeting of the aberrant transcription factor; however, this is a drug discovery challenge. A second approach would be to identify synthetic lethal relationships in the context of the aberrant transcription factor. THZ1, a covalent and potent inhibitor of CDK7, CDK12, and CDK13, kinases involved in transcriptional regulation, recently emerged as a targeted strategy to impair aberrant transcription. Extensive profiling of THZ1 against a diverse panel of >1,000 cancer cell lines revealed that the pediatric solid tumor, Ewing sarcoma, was exceptionally sensitive to this compound. We found that the anti-proliferative effects of THZ1 in Ewing sarcoma can be attributed primarily to CDK12/13 inhibition. Treatment of Ewing sarcoma cells with THZ531, a covalent and selective CDK12/13 inhibitor, decreased the phosphorylation of the C-terminal domain of RNA polymerase II, induced apoptosis, and markedly decreased colony formation capacity of Ewing sarcoma cell lines. In contrast, treatment with a selective CDK7 inhibitor had minimal effect. EWS/FLI is the transcription factor fusion protein that typically drives tumor establishment and maintenance in Ewing sarcoma tumors. Based on prior reports of this compound class inhibiting a small subset of highly expressed genes critical to tumor maintenance, we expected that these inhibitors would disrupt oncogenic EWS/FLI-driven transcription as the mechanism of inducing cell death. Surprisingly, however, global gene expression profiling revealed that THZ531 did not selectively repress EWS/FLI or EWS/FLI target genes. Rather, we observed that THZ531 preferentially repressed genes involved in DNA damage repair. Consistent with this finding, we found that THZ531 induced defects in DNA damage repair and highly synergized with DNA damaging agents that induce lesions repaired by homologous recombination (HR). Furthermore, we found that suppression of EWS/FLI attenuated sensitivity to THZ531 and the PARP inhibitor olaparib and abrogated synergy observed with this drug combination. Thus, we conclude that EWS/FLI establishes tumor cell synthetic lethality to CDK12/13 inhibitors by imparting sensitivity to DNA repair defects. This work establishes a novel mechanism of action of CDK12/13 inhibitors and gives further credence to the role of EWS/FLI in DNA damage response. Ongoing work is dedicated to the in vivo testing of THZ1 alone, and in combination with olaparib, as a novel targeted therapy for the treatment of Ewing sarcoma.

Citation Format: Amanda Balboni, Björn Stolte, Peter Kalev, Nicholas Kwiatkowski, Tinghu Zhang, Brian Abraham, Gabriela Alexe, Dipanjan Chowdhury, Richard A. Young, Nathanael S. Gray, Kimberly Stegmaier. CDK12/13 inhibition cooperates with the Ewing sarcoma oncoprotein EWS/FLI to attenuate homologous recombination repair in Ewing sarcoma cells. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2441.