Integrated Molecular Characterization of Patient-Derived Models Reveals Therapeutic Strategies for Treating CIC-DUX4 Sarcoma

Abstract

Capicua-double homeobox 4 (CIC-DUX4)–rearranged sarcomas (CDS) are extremely rare, highly aggressive primary sarcomas that represent a major therapeutic challenge. Patients are treated according to Ewing sarcoma protocols, but CDS-specific therapies are strongly needed. In this study, RNA sequencing was performed on patient samples to identify a selective signature that differentiates CDS from Ewing sarcoma and other fusion-driven sarcomas. This signature was used to validate the representativeness of newly generated CDS experimental models—patient-derived xenografts (PDX) and PDX-derived cell lines—and to identify specific therapeutic vulnerabilities. Annotation analysis of differentially expressed genes and molecular gene validation highlighted an HMGA2/IGF2BP/IGF2/IGF1R/AKT/mTOR axis that characterizes CDS and renders the tumors particularly sensitive to combined treatments with trabectedin and PI3K/mTOR inhibitors. Trabectedin inhibited IGF2BP/IGF2/IGF1R activity, but dual inhibition of the PI3K and mTOR pathways was required to completely dampen downstream signaling mediators. Proof-of-principle efficacy for the combination of the dual AKT/mTOR inhibitor NVP-BEZ235 (dactolisib) with trabectedin was obtained in vitro and in vivo using CDS PDX-derived cell lines, demonstrating a strong inhibition of local tumor growth and multiorgan metastasis. Overall, the development of representative experimental models (PDXs and PDX-derived cell lines) has helped to identify the unique sensitivity of the CDS to AKT/mTOR inhibitors and trabectedin, revealing a mechanism-based therapeutic strategy to fight this lethal cancer. Significance: This study identifies altered HMGA2/IGF2BP/IGF2 signaling in CIC-DUX4 sarcomas and provides proof of principle for combination therapy with trabectedin and AKT/mTOR dual inhibitors to specifically combat the disease.

CIC-Rearranged Sarcomas: An Intriguing Entity That May Lead the Way to the Comprehension of More Common Cancers

“…The CIC–DUX4 fusion proteins recognize CIC binding elements in target promoters and activate instead of repress gene expression via the DUX4 activation domain [ 23 , 37 ]. Indeed, the chimeric proteins transcriptionally activate the expression of several CIC target genes, including: the Polyoma virus enhancer activator ( PEA ) 3 family genes, which encode the oncogenic transcription factors ETV1 , ETV4 , and ETV5 ; Cyclin E1 ( CCNE1 ) and CCND2 ; MUC5AC [ 12 , 31 ]; and are associated with sustained activation of insulin-like growth factor (IGF) signaling [ 39 , 40 ].…”

“…Transcriptional analysis of CIC-DUX4-bearing human tumors and experimental models clearly indicate that these sarcomas are distinct from EWS [ 4 , 12 , 39 ] and may be more similar to other CIC-driven tumors. Drastic upregulation of target genes such as PEA3 family genes was indeed observed in other tumors due to deregulation of CIC functions.…”

“…Overall, all these mechanisms lead to rapid degradation/inactivation of CIC, thereby relieving repression of its downstream targets, including PEA3 gene family members. In addition to the CIC-ETV1/ETV4/ETV5 axis, molecular studies investigating additional CIC target genes have identified DUSP4 , DUSP6 , SPRED1 , SPRY4 , CCNE1 , CCND1 , and IGF2BP3-IGF axis [ 12 , 23 , 31 , 39 , 64 , 65 ]. The effects of CIC regulation of various target genes in the different tumors that are affected by CIC dysregulation have yet to be defined to verify whether convergence on key downstream nodes may be critical across these specific cancer subtypes.…”

“…Translational research on patient-derived models and/or genetically modified cells [ 12 , 23 , 24 , 39 , 40 , 66 , 67 ] has identified several new potential therapeutic targets and opened new potential avenues for therapy. Generation and genetic characterization of novel patient-derived CIC-DUX4 sarcoma xenografts and cell lines successfully highlighted the importance of the insulin-like growth factor 1 (IGF1)/IGF1 receptor (IGF1R) pathway in this tumor.…”

Lactobacillus rhamnosus HN001 Ameliorates BEZ235-Induced Intestinal Dysbiosis and Prolongs Cardiac Transplant Survival

“…BEZ235, an imidazo(4,5- c ) quinoline derivative, inhibits PI3K (p110-α, -β, -γ, and -δ isoforms) and mTOR kinase activity by binding to the ATP-binding cleft of these enzymes ( 6 ). BEZ235, with its dual PI3K-mTOR inhibitor activity, has been shown to have a significant antitumor effect on many cancers ( 7 , 8 ). BEZ235 has been found to inhibit the proliferation of multiple myeloma and contribute to apoptosis by inducing autophagy ( 9 ).…”