Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX; Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX.
Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX.
Cell Rep. 2018 Jul 3;24(1):238-251. doi: 10.1016/j.celrep.2018.06.006.
Identifying oncogenic drivers and tumor suppressors remains a challenge in many forms of cancer, including rhabdomyosarcoma. Anticipating gene expression alterations resulting from DNA copy-number variants to be particularly important, we developed a computational and experimental strategy incorporating a Bayesian algorithm and CRISPR/Cas9 "mini-pool" screen that enables both genome-scale assessment of disease genes and functional validation. The algorithm, called iExCN, identified 29 rhabdomyosarcoma drivers and suppressors enriched for cell-cycle and nucleic-acid-binding activities. Functional studies showed that many iExCN genes represent rhabdomyosarcoma line-specific or shared vulnerabilities. Complementary experiments addressed modes of action and demonstrated coordinated repression of multiple iExCN genes during skeletal muscle differentiation. Analysis of two separate cohorts revealed that the number of iExCN genes harboring copy-number alterations correlates with survival. Our findings highlight rhabdomyosarcoma as a cancer in which multiple drivers influence disease biology and demonstrate a generalizable capacity for iExCN to unmask disease genes in cancer.
在包括横纹肌肉瘤在内的许多癌症形式中，鉴定致癌基因和抑癌基因仍然是一个挑战。预计 DNA 拷贝数变异导致的基因表达改变尤为重要，因此我们开发了一种结合贝叶斯算法和 CRISPR/Cas9“迷你池”筛选的计算和实验策略，使疾病基因的全基因组评估和功能验证成为可能。该算法称为 iExCN，鉴定了 29 个横纹肌肉瘤驱动基因和抑制基因，这些基因富含细胞周期和核酸结合活性。功能研究表明，许多 iExCN 基因代表横纹肌肉瘤系特异性或共同的脆弱性。互补实验解决了作用模式的问题，并证明了在骨骼肌分化过程中多个 iExCN 基因的协调抑制。对两个独立队列的分析表明，携带拷贝数改变的 iExCN 基因数量与生存相关。我们的发现强调了横纹肌肉瘤是一种多种驱动因素影响疾病生物学的癌症，并证明了 iExCN 具有普遍的能力，可以揭示癌症中的疾病基因。
