SMARCA4 knockdown upregulates expression of myogenic genes in medulloblastoma. SMARCA4 knockdown upregulates expression of myogenic genes in medulloblastoma

SMARCA4 gene is mutated in a subset of Group 3 medulloblastomas. ShRNA mediated downregulation of SMARCA4 expression in three Group 3 medulloblastoma cell lines upregulated the expression of myogenic/muscle differentiation related genes as studied by the transcriptome analysis. Overall design: The expression of SMARCA4 was downregulated in a doxycycline-inducible manner in Group 3 medulloblastoma cell lines using the lentiviral vector tet-pLKO-puro. Total RNA was prepared from doxycycline-treated cells expressing the SMARCA4 shRNA and those expressing the vector alone and the parental cells . Libraries were prepared from the polyA-enriched RNA fraction using the Illumina Truseq RNA library preparation kit and sequenced on the Illumina Hiseq 2500 platform

SMARCA4基因在第3组髓母细胞瘤（Group 3 medulloblastoma）的一个亚群中存在突变。本研究通过转录组分析证实，在3株第3组髓母细胞瘤细胞系中，经短发夹RNA（short hairpin RNA，shRNA）介导的SMARCA4表达下调，可上调成肌/肌肉分化相关基因的表达。整体实验设计：本实验采用慢病毒载体tet-pLKO-puro，在第3组髓母细胞瘤细胞系中以多西环素（doxycycline）诱导的方式下调SMARCA4的表达。分别从经多西环素处理的转染SMARCA4短发夹RNA的细胞、仅转染空载体的细胞以及亲本细胞中提取总RNA。采用Illumina Truseq RNA建库试剂盒，以聚腺苷酸（polyA）富集的RNA组分制备测序文库，并在Illumina Hiseq 2500平台上完成测序。