Integrated molecular characterization of patient-derived models reveals therapeutic strategies for treating CIC-DUX4 sarcoma.

Capicua–double homeobox 4 (CIC-DUX4) rearranged sarcomas (CDSs) are extremely rare, highly aggressive primary sarcomas that represent a major therapeutic challenge. To identify selective therapeutic targets of CDS, we performed RNA sequencing of primary tumor samples from patients, patient-derived xenografts (PDXs) and PDX-derived cell lines and we highlighted an HMGA2/IGF2BPs/IGF2/IGF1R/AKT-mTOR axis that characterizes CDS. This highly active axis confers to CDSs sensitivity to both trabectedin, which prevents HMGA proteins from binding to IGF2BP2/3 promoters, and PI3K/mTOR inhibitor NVP-BEZ235 (dactolisib). Combined treatments with trabectedin and NVP-BEZ235 completely abolish the activation of the IGF2/IGF1R/AKT/mTOR axis and the in vivo growth of CDS tumors. The development of representative PDXs and PDX-derived cell lines models has helped to identify the unique sensitivities of CDS towards AKT/mTOR inhibitors and trabectedin, revealing a mechanism-based therapeutic strategy to fight this lethal cancer. Overall design: This study aims to identify a specific transcriptional signature that characterizes CDS in order to highlight selective therapeutic targets. For this goal we performed RNA-seq on four CDS and four EWS tumor samples along with PDXs, and corresponding cell lines. GSEA and leading edge analysis revealed a selective gene expression signature and molecular dependence of CDS on an oncogenic axis, whose functional relevance was assessed in PDXs and corresponding cell lines. These models presented a high correlation score with their original tumors based on gene expression profile, and maintain the phenotypic characteristics assessed by morphological and immunohistochemistry analysis. We tested the feasibility of CDS-derived PDXs and CDS PDX-derived cell lines to determine disease-specific pharmacological vulnerabilities and their usefulness to prioritize actionable drug targets in a timely manner. In particular, we tested their in vitro and in vivo chemosensitivity to two chemicals compounds, trabectedin and/or NVP-BEZ235 (alone or in combination), which target genes of the oncogenic axis that characterizes CDS, to offer a rationale for disease-driven treatments.

Capicua-双同源框4（Capicua–double homeobox 4, CIC-DUX4）重排肉瘤（CDSs）是一类极为罕见、恶性程度极高的原发性肉瘤，也是临床治疗的重大难题。为明确CDS的选择性治疗靶点，我们对患者原发肿瘤样本、患者来源异种移植瘤（patient-derived xenografts, PDXs）及PDX来源细胞系开展了RNA测序，鉴定出一条特征性的HMGA2/IGF2BPs/IGF2/IGF1R/AKT-mTOR信号轴。这条高活性信号轴可使CDSs对曲贝替定（trabectedin）及PI3K/mTOR抑制剂NVP-BEZ235（dactolisib）均产生敏感性：曲贝替定可阻断HMGA蛋白结合IGF2BP2/3的启动子区域。曲贝替定与NVP-BEZ235联合给药可完全抑制IGF2/IGF1R/AKT/mTOR信号轴的激活，并阻断CDS肿瘤的体内生长。具有代表性的PDX及PDX来源细胞系模型的构建，助力明确了CDS对AKT/mTOR抑制剂与曲贝替定的独特敏感性，为攻克这类致死性癌症提供了基于分子机制的治疗策略。本研究整体设计：旨在鉴定CDS的特异性转录特征，以明确其选择性治疗靶点。为此，我们对4例CDS肿瘤样本、4例尤因肉瘤（Ewing sarcoma, EWS）肿瘤样本，以及对应的PDX和细胞系开展了RNA测序。通过基因集富集分析（Gene Set Enrichment Analysis, GSEA）及前沿基因分析（leading edge analysis），我们鉴定出CDS特异性的基因表达特征及致癌信号轴依赖特性，并在PDX与对应细胞系中验证了该信号轴的功能相关性。上述模型与原始肿瘤的基因表达谱相关性较高，且通过形态学与免疫组化分析保留了原肿瘤的表型特征。我们验证了CDS来源PDX及PDX来源细胞系用于鉴定疾病特异性药理脆弱性的可行性，以及其用于快速筛选可靶向药物靶点的价值。具体而言，我们在体外与体内测试了CDS模型对两种靶向CDS特征性致癌信号轴相关基因的化学药物——曲贝替定和/或NVP-BEZ235（单药或联合给药）的化疗敏感性，旨在为该疾病的靶向治疗提供理论依据。